FNIA 3D is a game that enhances the player experience with more nights and customizable options. The storyline is enriched with 3D graphics, allowing detailed views of anime-inspired characters. As players progress through levels and defend against the attacks of these animated robots, they unlock various bonuses, including a secret night.

The gameplay mechanics in FNIA 3D are inspired by the original FNAF horror game. The player takes on the role of a night guard in a facility where robotic dolls become active at night. To survive their attacks, the player can use cameras, doors, and a flashlight. However, the use of this equipment is dependent on a limited supply of electricity, which varies for each level. The challenge intensifies as the game progresses, with reduced availability of electricity and increased activity from the animatronics.

In Five Nights in Anime 3D, after completing the main story, players gain access to the Custom Night mode. This mode allows players to design their own night by adjusting the activity levels of the animatronics, adding a personalized challenge to the gameplay. Additionally, a bonus menu becomes available after completing the fifth night. This menu includes cheats that remove electricity limitations, enable a fast night mode, or provide a radar for tracking animatronic movements.