20 Popular Jon and Daenerys Fanfiction Stories to Read in 2024

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If you are looking for some of the best Jon and Daenerys fanfiction — you have come to the right place! 

Jon and Daenerys are perhaps the most famous couple from the world-famous series A Song of Ice and Fire, but you may know it as Game of Thrones.

The book series A Song of Ice and Fire has been adapted into the television series Game of Thrones, and it is one of the most popular television shows of all time. 

It is revered worldwide, and just about everyone has at least heard of this show, even if they know nothing about it. 

This series is full of violence, explicit scenes, and other adult content, and the fanfiction stories below are no different. 

The television show and the book series are targeted at adults, and the same caution should be taken for the stories below. 

This article will explore some of the most popular Jon and Daenerys fanfiction on AO3. 

Keep reading to learn more. 

1. The Last Hope for Westeros

First up is a Jon and Daenerys fanfiction that has been in the works for years. 

The White Walkers have won in this fanfic, and all hope seems lost. 

Jon gets a gift from the gods to return in time and save everyone from their devastating future. 

While he is time traveling, Jon decides to go to Pentos to save his true love, Daenerys. 

He reclaims the Iron Throne with Daenerys, and the two unite the Seven Kingdoms. 

But no time travel is ever without consequences, and Jon and Daenerys are not ready for the effects of these changes. 

This story has everything you could want in a Jon and Daenerys fanfiction, including action, passion, and war. 

It is a famous story for good reason. 

2. My Father’s Son

Next up is a Jon and Daenerys fanfiction that is one of the more explicit. 

This story has a lot of mature romantic content, violence, and death. 

Check out some specific content warnings before getting too far into this story. 

This story focuses on Rhaegar and Lyanna, so it is a bit of an alternate universe. 

Jon and Daenerys also feature in this story, but their romance is not the main focus. 

Rhaegar is a brooding prince who is living a lie about his father’s ability to rule. 

After he is forced to marry Lyanna, his heart begins to soften, and we see a new side of this once-troubled man. 

He must confront the lies that haunt him and make difficult decisions. 

This story is unique in that it features lesser-known characters, and we get to see what the story might have been like if they had lived. 

3. The Raven’s Plan

The next Jon and Daenerys fanfiction that we will look at is another story involving time travel. 

In this fanfic, the Second War for the Dawn is over. 

The Others win, and our protagonists seem to have no hope.

That is until one person concocts a unique plan that might save them all.  

This story involves a lot of death, as you can expect for a tale in this genre, but there are a few deaths you will not see coming. 

Don’t worry — plenty of romance and romantic tension intertwine with the action and fighting. 

Though Jon and Daenerys’ relationship is not at the forefront of this story, it is still an essential element that adds to it. 

4. Wolf of Númenor

Jon Snow’s decade-long journey leaves him far from the icy clutches of the North. 

He seeks solace and companionship among the noble lords and ladies of Highgarden amidst the fragrant roses of the Reach. 

He also captures the heart of a golden rose, and a love blooms despite thorny politics.

However, the relentless fires of war rage across Westeros, sparing no beauty or kindness in their path. 

In this crucible of chaos and change, Jon Snow embraces a rebirth. 

His path leads him to unknown lands, far from Westeros’ shores, yet he will discover something remarkable among these newfound compatriots.

Jon will forge connections deeper than any castle’s moat in these foreign lands, finding kinship, love, and acceptance beyond borders and banners. 

5. Lies

In this Jon and Daenerys fanfiction, we primarily focus on Jon and Ned. 

Daenerys is still an integral player in this story, but her relationship with Jon is not at the forefront. 

In the world of this story, Ned Stark avoids execution and gets a second chance in life, leading him to join the Night’s Watch. 

He arrives at the Wall just in time to tell Jon the truth about his mother. 

As we know, this is a startling truth that changes Jon’s life. 

It is interesting to see how Ned can change the course of the story and bring new life to a critical plot point. 

At some point, just about every Game of Thrones character appears in this story, so you can glimpse all your favorites throughout the tale! 

6. An Empire of Ice and Fire

This Jon and Daenerys fanfiction starts where the TV show picks up in season 1.

However, the author of this story quickly takes it in a new direction. 

In this story, Jon and Daenerys meet much earlier, and their relationship is as tumultuous as ever. 

They have much more time to develop and establish their relationship, changing the story. 

Amid this budding romance, a simple twist of fate takes Jon and Ned on a journey that changes everything. 

This story is full of twists and turns, and the author takes the story we love and gives it a revamp.

The characters remain very true to who we know them to be, but now they face new enemies and relationships. 

This exciting story contains all the violence and mature content you could ever want in a Game of Thrones fanfiction. 

7. Her Life and Her Death

If you want a slow-burn romance from your Jon and Daenerys fanfiction, this is the story for you. 

This fanfic’s romance is slow to develop and full of tension. 

It begins with baby Daenerys and young Jon growing up in different environments. 

It covers the events of many years, and we get to see how Jon and Daenerys become the people we know them to be. 

You can consider it a bit of a coming-of-age story, but there is still plenty of violence and death throughout their upbringings. 

As the Great Game commences across the sea, the fate of Westeros changes forever. 

8. Our Choices Seal Our Fate

In this Jon and Daenerys fanfiction, the alternate universe we enter might make your head spin. 

In this world, there is no Battle of the Trident, and Rhaegar soon takes over the throne from his father. 

Everything in the kingdom quickly goes south, and there seems to be no way to fix it. 

Jon goes to war with his dead mother’s family, and we see how different things are. 

This world is new, with characters taking on unique and unexpected roles. 

There are new alliances and relationships, though some of our favorites remain the same. 

This story is unique and unlike any other. 

9. Home

Next up is a Jon and Daenerys fanfiction that gives new life to season 8 of Game of Thrones. 

The author of this story begins at the end of the 7th episode of season 7 and explores some possibilities and new realities that could have replaced the events of season 8. 

For those who didn’t like the 8th season of the show, this is a great story to get a new take on it.

In this story, Jon and Daenerys travel northward to fight for their people, home, and each other. 

Many of our favorite characters appear in this story, though they make decisions and choices that are slightly unusual. 

This story focuses heavily on Jon and Daenerys’ romance.

It is an excellent choice if you want to see their relationship grow and blossom. 

10. A Song for Dragons

In this story, winter is coming yet again, and summer is coming to a close with a quickening pace. 

Jon travels across the Narrow Sea and finds himself walking a path that brings him into conflict with a cruel dragon prince. 

This prince is willing to sell his sister for access to the Iron Throne, and thus begins the story of Jon and Daenerys. 

This story features countless different characters, and they are all written well. 

The author of this story has a knack for writing dialogue and conflict without coming off as forced or unrealistic. 

11. Dragons in Winter

In her unyielding quest for knowledge about her beloved dragons, Daenerys Targaryen embarks on an epic journey to the Wall, seeking wisdom from the one man who might hold the answers.

At the formidable Wall, she crosses paths with Jon Snow, the remarkable 998th Lord Commander of the Night’s Watch.

But their fateful meeting occurs against a dire backdrop — enemies surround the Wall. 

Lord Commander Snow relentlessly struggles to protect its sanctity and rescue the Night’s Watch from its internal turmoil. 

Can he muster the strength and allies necessary to fortify the Wall and safeguard the realm against the looming existential threat?

The fate of an entire kingdom hangs in the balance as Daenerys Targaryen and Jon Snow must navigate the treacherous waters of power, politics, and the ever-present specter of an ultimate, otherworldly enemy.

12. The Conspiracy of Ice and Fire

In this Jon and Daenerys fanfiction, Jon Snow grows up hidden from the world’s prying eyes. 

In the shadows, a covert group tirelessly prepares Westeros for the triumphant return of the Targaryen dynasty. 

As Jon reaches the age of maturity, he begins to take control of his destiny, embracing the weighty burden of his birthright.

But his journey isn’t just about claiming the throne — it’s about claiming his place in a world that teems with political intrigue, supernatural forces, and the grandeur of dragons. 

Yes, dragons! 

Unlike the canon story, where Daenerys reigns as the Mother of Dragons, Jon inherits these majestic beasts.

Meanwhile, Daenerys’ life takes a drastically different trajectory. 

She’s yet to embark on her epic conquest of Essos, and the road to becoming a dragon rider is long and arduous. 

Together, they rule the Seven Kingdoms, rewriting the history of Westeros and ushering in an era where dragons and humans coexist in harmony.

It’s a tale of two intertwining destinies, fire and ice converging, and a realm reborn under the rule of two true equals.

13. The Winter King and the Queen of Summer

This Jon and Daenerys fanfiction reimagines a pivotal moment in the Game of Thrones universe at the beginning of Jon Snow’s journey. 

Instead of solemnly reciting his Night’s Watch oath, Jon receives a mysterious raven’s message that unravels the very fabric of his identity. 

This revelation isn’t about pledging his life to the Night’s Watch — it’s about staking his claim to a robust and blood-soaked legacy.

He learns that he’s not just the illegitimate son of Eddard Stark but rather the rightful heir to the Iron Throne, a Targaryen prince.

With a newfound purpose, Jon’s journey takes a wildly different turn. 

Instead of wandering beyond the Wall, he sets his sights on the iron seat of Westeros. 

He’s no longer just a bastard — but he’s a dragon-blooded contender with a desire to rule.

This transformation sends shockwaves through the Seven Kingdoms. 

The Game of Thrones has a fresh and fiery player, and Jon’s quest for his crown promises intrigue, conflict, and a power struggle of epic proportions. 

His journey now entwines with the fiery legacy of House Targaryen, reshaping the destinies of all who cross his path. 

The winds of change are blowing, and Jon Snow is no longer just a watcher — he’s a contender for the ultimate throne.

14. I Fear No Fate (For You Are My Fate, My Sweet)

The next Jon and Daenerys fanfiction features other couples, mainly Myrcella Baratheon and Robb Stark.

Myrcella Baratheon bears the weighty knowledge that her destiny intertwines with the cold, unforgiving world of politics. 

But she didn’t see this unforeseen twist of fate that would propel her into the heart of the North at the tender age of eight. 

Little did she know that this northern escapade was the first step in a journey that would ultimately lead her to the side of the formidable Robb Stark, forever altering the course of her life.

In this swirling whirlpool of alliances, loyalties, and the ever-present shadow of war, Myrcella Baratheon’s story is far from ordinary. 

The tale of her transformation from a pawn in a political game to a critical player in a northern saga is a testament to the unpredictable nature of life in the Seven Kingdoms. 

Winter is coming, and Myrcella is ready to face it head-on.

15. Live as a Wolf or Die as a Dragon

In this Jon and Daenerys fanfiction, while on a journey, Jon Snow has a revelation ready to reshape the course of the fate of the Seven Kingdoms.

He isn’t about to make his grand return to his ancestral home. 

No, he is returning as Aegon Targaryenthe true dragon-blooded heir, set to emerge from the cold North and into the hearts and minds of the Northern folk.

Imagine the waves of shock and awe rippling through Winterfell as the news spread like wildfire. 

Aegon Targaryen, the long-lost scion of House Targaryen, is arriving, and he doesn’t only have a claim to the Iron Throne but also the fire of a dragon’s lineage coursing through his veins. 

The North, a land famous for its rugged loyalty to the Stark name, suddenly finds itself with a dragon in their midst.

Will Jon embrace his destiny as Aegon Targaryen, or will he remain the steadfast Jon Snow? 

The answer to that question will shape not only his future but the destiny of the entire realm.

16. A Jade Dragon

Once Jon Snow, now Daeron Targaryen, learns the truth about his heritage, he embarks on a journey eastward. 

However, fate has different plans for him as he finds himself lost in the land of Yi-Ti, far from the familiar landscapes of Westeros. 

But Jon isn’t alone in this foreign territory.

He discovers a realm of ancient traditions, mysterious cultures, and looming dangers. 

The people here are unique, their customs as diverse as the colors in a rainbow. 

It’s a new world worth exploring, but Jon has more pressing concerns than curiosity.

He remains ever vigilant about the dangerous threat beyond the Wall. 

After all, Jon knows that, sooner or later, he must return to the frigid North, where the relentless Long Night threatens to descend again.

But Jon isn’t planning to face this impending darkness alone. 

In Yi-Ti, he aims to forge alliances, gather allies, and amass the strength to confront the relentless forces of the Long Night.

The tale of Jon’s adventures in Yi-Ti is just beginning, promising to be an epic chapter in the ongoing ice and fire saga.

17. Red Rubies

While visiting Ned Stark, Jon Arryn carries a proposition that would reshape the fate of one young boy — Jon Snow.

As the two men engage in a conversation heavy with implications, Jon Arryn lays out his offer: the opportunity for him to foster Jon Snow in the Vale under the careful guidance of Arryn himself. 

The Vale, a land of breathtaking beauty with its towering mountains and picturesque valleys, is famous for its courtly traditions, martial excellence, and strong ties to House Arryn. 

It’s an environment that starkly contrasts the harsh, unforgiving winters of the North. 

Jon Arryn argues that this change could provide Jon Snow with invaluable exposure to a different world, a chance to hone his skills, and, perhaps most importantly, protection from the political machinations around him.

Ned, ever the father figure, must weigh the risks and benefits of sending Jon Snow away. 

It’s a moment of reckoning that will shape the future of a young bastard who knows nothing of the world beyond the Wall.

18. The Second Targaryen Dynasty

In the heart of the Red Keep, amidst the towering spires and whispered intrigues of King’s Landing, Jon and Daenerys share a secret that could change the fate of Westeros. 

They aren’t just childhood companions — they are star-crossed lovers with their hearts intertwining like dragons in the sky. 

But as their affection grows, a shadow looms over their love story — King Rhaegar’s ambitious plans.

As whispers of their love grow louder, so do the threats against them. 

Enemies begin to conspire, casting their ominous clouds over the young couple. 

How will Jon and Daenerys navigate the treacherous waters of intrigue and power, all while safeguarding their love from prying eyes and evil forces?

Find out in this thrilling Jon and Daenerys fanfiction!

19. The White Wolf and the Dragon Queen

This Jon and Daenerys fanfiction offers a riveting glimpse into the Game of Thrones, where alliances crumble like sandcastles and character fates hang in the balance. 

It gives us a unique perspective of each character, including Jon, Dany, Sansa, Bran, Arya, Tyrion, Jaime, and Samwell — showing readers their POV.

While predominantly grounded in the show’s spectacle, this narrative doesn’t shy away from George R.R. Martin’s canon written word and the Telltale series.

It’s a saga where the echoes of past seasons reverberate through to the present, forging new alliances and ringing the death bell for cherished figures. 

From the icy North to the fiery South, the world of Westeros is a cauldron of chaos, and the Game of Thrones is far from over.

20. Dragons of Ice and Fire

Did you ever wonder what it would be like if Jon Snow were a dragon?

Well, in this Jon and Daenerys fanfiction, you can find out. 

Jon faces the White Walkers, discovering a power that might change his life and the world around him. 

He journeys south as a dragon, and he sees the world begin to shift. 

This story is dark and violent but very well-written and engaging. 

It differs from many other stories, and the romance takes a bit of a backseat to other plot lines. 

Jon and Daenerys Fanfiction: Conclusion

I hope this article has helped you find some great fanfiction featuring romance from this couple!

These are just a tiny sample of all the fantastic stories.

So be sure to look and find your favorite among them.

And if you have questions about this topic, feel free to leave a message in the comments below!

Lastly, if you want to read more top fanfiction posts on this blog, then check out:

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