One of the most obvious checkpoints is the elevator.
The checkpoints in One Leaves are locked gates connected to puzzles by red wires. The gates open after you’ve completed the puzzles in that level. Once the switches to each puzzle have been activated, the checkpoint opens and you can proceed to the next area in the game. When the gate opens, the scoreboard shows which your standing in the game (first through fourth).
There are two checkpoints in the game. One in the school and one in the hospital.