Extreme Speed/fake out Pokemon are generally good at dealing with Prankster. Taunt is even better. In fact, taunt can force a switch in. I find leading with one of the above options is almost necessary in the meta game.
Substitute is a slow option, but a viable one. It makes setting up on a Prankster easy. I always have a priority counter Pokemon on my team just in case I encounter an annoying prankster, and that works for me. My personal choice is Gastro Acid on my contrary Serperior. Contrary inverts any stat debuff while using gastro acid removes prankster (and kills mega kangaskhan, mirror match Serperior, Protean Greninja, and a many other key threats). After prankster is gone, leaf storm becomes the go to move, unless you run an appropriately typed check. Of course, if the opponent is running substitute, you can just sit on leaf storm until they try to heal or can't make anymore.
Finally; synchronize, confuse ray, thunder wave and type checks are good improv choices.