The game was originally going to be called "The Butt Hole of Time", however after being told that retailers wouldn't allow the term "butt hole" to be sold on shelves, the series creators, Trey Parker and Matt Stone, instead decided on "The Fractured but Whole".

To improve on the previous game, The Stick of Truth, series creator, Trey Parker, watched YouTube let's player PewDiePie's run of The Stick of Truth to see what worked and what didn't.

According to Trey Parker and Matt Stone, the script for Fractured But Whole is over 360 pages, the size of two feature film scripts.

If the player tries to enter a code in the game without getting it first, Cartman will appear dressed up as Patriots coach Bill Belichick and will comment the following.

"Hey Tom Brady, do you wanna play the game or do you wanna be known as a smug cheating bitch the rest of your life?"
"Okay so I guess you wanna Tom Brady through the whole game, what's the matter? Can't do it on your own?"
"Is this fun for you, Tom Brady?"
"You broke the rules rules rules"

This is a reference to the South Park season 19 episode "Stunning and Brave".

Most of the cut-scenes in the game are skippable, but the opening cut-scene is a special case. If you try to skip it the first few times, Cartman will chastise you for doing so and the cutscene will continue to play. If you continue to try the skip the cutscene, Cartman will finally give in. However, it'll go straight to the closing credits instead.

Within the game's files is an image of Mr. Garrison with a filename listing him as an ally, implying he was originally meant to be a summon. It's possible he was scrapped to keep in continuity with the show at the time, as he would be running for and elected president of the United States over the course of seasons 19 and 20.