Which fuse controls power windows on 1999 ford explorer?

There isn't a single fuse solely dedicated to power windows in a 1999 Ford Explorer. The power windows are usually controlled by a fuse and a relay. The exact fuse and relay location will depend on your specific Explorer's options (e.g., if it has heated mirrors, which sometimes share a fuse or circuit).

To find the correct fuse, you must consult your owner's manual. It will have a fuse box diagram showing which fuse(s) relate to the power windows. The diagram will also show the fuse amperage.

Without your owner's manual, I cannot give you the correct answer. Attempting to locate the fuse without the diagram risks damaging other systems by pulling the wrong fuse.