Preheat oven to 375 degrees and cover two baking trays with parchment paper so puffs won't stick.
In large saucepan, bring water, salt, and butter to a boil.
Once butter is melted add the flower and stir for 20-30 seconds until the dough forms and stops sticking the pan. Reduce heat and set aside for 5 minutes until cool.
Beat in eggs one at a time, along with comte cheese, diced thyme and black pepper. Mix thoroughly.
Place large teaspoonfuls of mix onto baking sheets about 1 inch apart.
Bake for 20-25 minutes; make sure to rotate trays halfway through cooking process.