In Scary Teacher 3D, players take on the role of a student seeking revenge on their cruel teacher. The core gameplay involves navigating the teacher's house in first-person view, solving environmental puzzles to set up elaborate pranks. Success requires stealth to avoid detection while exploring rooms and interacting with objects.

The touchscreen controls are used for movement, looking around, and selecting items. Gameplay is mission-based, with each level presenting new objectives and prank setups. Players must observe the teacher's patrol patterns and use the household items they find to complete their plans without getting caught.