Preheat the oven to 350 degrees F (175 degrees C). Line a cookie sheet with parchment paper or use cooking spray.

Combine peanut butter, honey, and brown sugar in a large bowl; beat with an electric mixer until creamy. Add Greek yogurt, egg, and vanilla extract; mix well. Add whole wheat flour, baking soda, and salt. Mix until dough is blended together. Refrigerate dough for 20 minutes.

Scoop 1 tablespoon of chilled dough and roll into a ball. Place cookie balls 2 inches apart on the prepared cookie sheet. Press down with a fork in a criss-cross pattern.

Bake in the preheated oven until edges firm up and start to brown, 8 to 10 minutes.