In the North American Version of the game, Emiya Alter's skin tone is lighter than in the Japanese Servers. This was done out of concern players would associate him with any racist stereotypes, but was also met with criticism that the change went against his backstory, in which his grayish black skin color (as well as changed hairstyle and eye colors) was the result of rebound effects from overuse of projection magecraft, burning his skin and distinguishing him from the original Emiya whose skin was already naturally tanned.

The original plan for the game was a PvP, online MMO game known as Fate/Apocrypha. However, these plans were cancelled early in development. The project was later revived as "Fate Online Project Reboot" on the behest of publisher Aniplex wanting to make a mobile game to promote the Fate IP. According to head writer Kinoko Nasu, he never owned a smartphone prior to the development of Fate/Grand Order, but got one and played various free-to-play mobile games for reference. Fate/Apocrypha itself would later be revived as a Light Novel series.

Throughout the second part of Lostbelt 6, Avalon La Fae, the player is met with several unskippable dialogue options. Special dialogue options can be unlocked by selecting the following options:

• Section 11-6: Spoiler:"...(Does that mean Altria's and Oberon's eyes are-)"
• Section 12-1: Spoiler:"(Even from so early on...?)"
• Section 13-1: Spoiler:"Come to think of it, you never did tell us about your summoning, Oberon."
• Section 16-5: Spoiler:"...(There's something I should double-check with Oberon...)" Choosing this option also reveals an extended sequence where Oberon reveals he hired Koyanskya to take care of Morgan's reinforcements during the siege of Londinium.
• Section 20-4: Spoiler:"...(But, if I do that...)"
• Section 23-4: Spoiler:"...Maybe it's because she can tell when someone is lying?"
• Section 23-6: Spoiler:"Even though you said it doesn't exist here?"

By selecting these options when prompted, special red dialogue options appear after beating Spoiler:Cernunos and Spoiler:Grimr The Sage declares himself the only Servant summoned from Proper Human History. These red dialogue options reveal that the player figured out Oberon was tricking them into playing along with his scheme, and that he was lying about his motives and goals the entire time.

The "Fate/Unpublished Material" and "Fate/Side Material" booklets reveal an unused character for Fate/Stay Night. "Tachie", otherwise known as "Galahad", "Shielder", or "Stray Servant" was planned as an alternate Heroine Servant the player could have chosen instead of Saber. She was scrapped from the game as to keep the story manageable.

This character was also planned for the animated adaptation of Fate/Stay Night by Studio Deen, but was scrapped in favor of an adaptation of the "Fate" Route. An animated movie featuring Tachie was also considered, but also abandoned.

This unused character was later revisited and inspired the design for Mash Kyrielight, a seperate Shielder Servant and primary heroine of Fate/Grand Order.

In the Fate/Grand Order material IV book, artist Shimaudon details their experience designing Nitocris. Of note, it is revealed that Nitocris was initially planned to be a 3-Star Servant, but was changed to be a 4-Star. This decision also led to her third ascension being altered to be more revealing.

After clearing Chapter 22 of Lostbelt 5: Olympus, Spoiler:Miyamoto Musashi will be removed from the Spirit Origin List in the Material (Servant) list under My Room. In the place of her original Saber and Summer Berserker form is a dimmed, glitched-out icon reading "DATA LOST". This reflects the story events as Musashi sacrificed her existence in order to seal away Chaos.
This change is purely cosmetic; Spoiler:both forms of Miyamoto Musashi can still be used in regular gameplay, rolled for in rate-up banners, and otherwise interacted with via Servant Inventory and as the selected Favorite in My Room.

In Episode 45 of "More Learning With Manga! Fate/Grand Order", Gudao (The Male Master) contemplates whether he should use a Holy Grail to increase Astolfo's Level Cap, or save it for when he gets a Limited 5-Star Version, presumably as a Saber Class. The Fifth Christmas Event "Nightingale's Christmas Carol" would introduce exactly that: a new, Limited 5-Star Saber version of Astolfo.

In Episode 1 of the satirical manga series "More Learning with Manga! Fate/Grand Order", Gudako (The Female Master) is depicted deleting and reinstalling the game Spoiler:in order to bring Olga Marie, who died during the Prologue of the game, back from the grave.
Coincidentally, near the end of Lostbelt 5 Part 2: "Olympus", Spoiler:Olga Marie is brought back as U. Olga Marie, the vessel of the Foreign God responsible for the destruction of Humanity and formation of the Lostbelts.

The Chinese Version of Fate/Grand Order, published by video sharing website bilibili, features several changes and censored elements compared to the original Japanese release. These were all likely done as to comply with Chinese law. Some examples of changes are as follows:

• Boudica: Attire altered to reduce cleavage and panties were changed into shorts. She and Mata Hari also temporarily had their portrait artwork removed before being put back in place
• Shuten-Doji: Ascensions were altered to reduce visible skin throughout.
• Mata Hari: Bikini top was made larger to reduce cleavage. She and Boudica also temporarily had their portrait artwork removed before being put back in place
• Cú Chulainn: Second Ascension was altered to cover his chest.
• Minamoto-no-Raikou: The cloth covering her breasts in her first ascension is retained in her second and third.
• Hassan of the Cursed Arm: Second Ascension adds a cloth obscuring his face and chest.
• Yu-Mei-Ren (Assassin): Name was temporarily changed to Assassin 230, then later 雏罂. Reduced the size of her cleavage window and added fabric to hide skin showing in her second and third ascensions. Her bust size is also notably smaller in the Chinese version.
• Yu-Mei-Ren (Lancer): Swimsuit was adjusted to be less revealing.
• Gorgon: Attire adjusted to cover chest more.
• Wu Zetian (Assassin): Name was temporarily changed to Assassin 170, then later 周照. All appearances of the character were scrubbed, as well as any mentions of her by name, replacing her with the default Assassin Card. Spoiler:This affects the story of Agartha as she is the true identity of Assassin of the Nightless City, one of the story's antagonist. Was later given fabric covering her stomach on her second, third, and final ascensions.
• Xuanzang Sanzang: Cleavage is covered. Artwork was temporarily disabled until adjusted artwork was provided. Was renamed "Pilgrim To The West" (西行者) to comply with Chinese depiction laws.
• Yang Guifei: Second ascension adds frills to her attire's lower body, while her third and final cover up her chest. She also had some of her ascensions disabled until new artwork was added.
• Orion (Artemis): Removed cleavage from first ascension artwork and icon.
• Carmilla (Assassin): Added clothing to areas otherwise not covered in the original version.
• Ushiwakamaru: Was given skintight clothing covering her torso. Coincidentally, this resembles her design in Melty Blood: Type Lumina, which was also censored in a similar fashion.
• Tamamo Cat: Reduced cleavage and bust size.
• Fergus Mac Róich: Added bandages covering his chest.
• Phantom of the Opera: Blood was removed from his second ascension's knives.
• Giles De Rais (Saber): Blood stain removed from his second ascension.
• Scáthach (Lancer): Skin Tight suit made less see through.
• Darius III: Body paint was removed and his expression was changed to be less angry.

In addtion, several other Chinese-originating Servants had their names changed to their Class, followed by their Servant ID. Other Servants also had their names changed. Jack The Ripper, for example, was changed to "Abandoned Son of the Mist." Similar changes were also made to various Craft Essences, similarly removing revealing clothing and references to blood.