The choice of recruiting Arran and Samson from "Fire Emblem: Shadow Dragon and the Blade of Light", and its DS remake, inspired the idea of the player having to choose a kingdom in Fates.

On December of 2012, Shin Kibayashi was approached to write the Birthright storyline. He almost refused the offer due to his work schedule, but after playing through a copy of Awakening with his daughter, Kibayashi decided to accept and wrote an initial draft story.

Despite his initial commitment of a ten-page summary for each storyline, he became fond of the characters and the full summary for Birthright extended to 500 pages. After delivering his work, he then wrote summaries of equal length for Conquest and Revelation, driven by the need to create a high-quality story.

The game's theme song, "If~ One's Thoughts", was sung by Japanese pop singer Renka, who also provided Azura's in-game singing voice. After hearing Renka's audition, the developers instantly decided that she was right for the role. According to music personnel, several among them cried when they first heard the song.

The game's Japanese subtitle, "If", came from the amount of choices featured for players in the game. The English title "Fates" referred to the concept of the main character shaping and changing their fate by choosing a side.

The development team reviewed how fans and critics had responded to Fire Emblem: Awakening and saw that the story had been criticized for its quality by the main fan base despite its approval from new players. This inspired the team to write a story for Fire Emblem Fates that would appeal to series veterans and newcomers alike.

The concept for different versions of the game originated from Producer Hitoshi Yamagami's memories of the first Fire Emblem, which allowed for choosing different protagonists but did not change the story. The team decided to create multiple versions of the game, wanting to play from both sides of a conflict and show both sides as neither good nor evil. Their initial plan was to include a single choice between one kingdom or the other, but Yamagami wanted a neutral path where neither side was chosen, so a third version of the game was planned as DLC.

After the creation of the three storylines, the team decided to publish Birthright and Conquest as separate physical releases. This was because packaging them as a single release would have required selling the game at a two-game bundle price, which would have been unfair to people who only wanted to play one version. Another reason for this decision was how easy it had become to include the other versions as cheaper downloadable content.

While the Japanese titles for Birthright and Conquest were written in kanji, the third storyline's title was written in katakana to distinguish it from the other two.

Fire Emblem Fates is the first Fire Emblem game to include the option to foster same-sex relationships. Potential male and female partners appear in Conquest and Birthright, respectively, and both appear in Revelation. According to Nintendo, this move was done to reflect the diversity of their player base.

The choice of making Corrin barefoot was made early on to reflect on the more "animalistic" nature of their dragon heritage.

If Takumi is reclassed to a Swordmaster, he has a unique model where he can be seen wearing Spoiler:the armor of his deceased father, Sumeragi.