Preheat oven to 425 F. Spray a large baking sheet with cooking spray.

Stir together water, butter and salt in a saucepan; bring to a simmer. Reduce heat to medium; whisk in flour and stir vigorously until a paste-like dough forms. Transfer to a bowl to cool until warm.

Beat in one egg, thyme and pepper into cooled dough with a wooden spoon until egg is completely incorporated. Add remaining egg and beat until completely incorporated. Stir in remaining cheese into dough.

Scoop 1 inch balls of dough and set 2 inches apart onto baking sheet. Top balls with cheese.

Bake until dough is puffed, lightly golden, and appears dry, about 15 minutes.