How long do you microwave Hot Pockets. A Hot Pocket should be microwaved for two minutes. Most of the time Hot Pockets will be molten hot and frozen at the same time when microwaving. If you want to avoid this, just microwave your Hot Pocket for 1:30, carefully hold the Hot Pocket at both ends (be careful not to burn yourself or spill the filling) and shake it so that the hot and cold areas mix. Microwave for the remaining :30 and enjoy your perfectly cooked Hot Pocket.