Preheat Oven & Prep Pan. To start, preheat the oven to 350 degrees F. Line a metal 8x8 baking pan with parchment paper and set aside.
Cream Butter & Sugar. In a large mixing bowl or the bowl of a stand mixer, cream butter, brown sugar, and granulated sugar 2-3 minutes until light, fluffy, and creamy. Scrape down the sides of the bowl.
Add Egg & Vanilla. Next, add the egg, then the vanilla, mixing until fully incorporated.
Add Dry Ingredients. Scrape down the sides of the bowl and add gluten-free flour, baking soda, and salt. Mix until almost fully blended, with just a few floury patches left.
Add In Chocolate Chips and mix until just fully combined and no dry patches remain. The cookie dough will be softer than what you might be used to, but DON'T add extra flour! This softer, more batter-like texture is what helps it bake evenly.
Divide Dough. Using rough estimates (this doesn't need to be perfect), divide the dough so you have 2/3 of the dough set aside for the bottom layer and 1/3 of the cookie dough for the top.