Preheat your oven to 350°F. Line a 9x9-inch baking pan with parchment paper and lightly grease if needed.
In a medium saucepan over medium heat, melt the butter for the cookie layer. Continue cooking, stirring frequently, until the butter becomes golden brown and smells nutty, about 3–5 minutes. Remove from the heat and let cool for 10–15 minutes.
In a microwave-safe bowl, melt the butter and chocolate chips together until smooth.
Whisk in the granulated sugar and brown sugar until combined. Add the eggs, egg yolk, and vanilla extract and whisk until the mixture looks glossy and smooth.
Fold in the flour, cocoa powder, and salt until just combined. Do not overmix.
Pour the brownie batter into the prepared pan and spread evenly.
In a large bowl, whisk together the cooled brown butter, dark brown sugar, and granulated sugar until smooth.
Add the egg, egg yolk, and vanilla extract and mix until combined.
Fold in the flour, baking soda, and salt until just combined, then stir in the chocolate chips.
Scoop large pieces of cookie dough over the brownie batter. Lightly press the dough into the batter.
Use a knife or spatula to gently swirl a few areas together for a bakery-style look. Avoid fully mixing the layers.
Bake for 32–36 minutes, or until the edges are set and the cookie tops are lightly golden. The center should still look slightly soft.
Allow the brookies to cool in the pan for at least 30 minutes before slicing. Serve warm or at room temperature.