Preheat the oven to 325°F. Line an 8x8 or 9x9 square pan with parchment paper.
To make the cookie layer; in a medium bowl or the bowl of a stand mixer, mix the butter, brown sugar, and sugar. Add the egg and vanilla, and mix until combined.
Add the flour, baking soda, and salt, and mix to form a soft dough. Gently fold in the chocolate chips. Refrigerate until ready to use.
To make the brownies, in a large bowl, whisk the butter and sugar. Add the eggs and vanilla, and mix until smooth. Add the flour, cocoa powder, baking soda, and salt, and mix until just combined. Fold in the chocolate chips.
Spread the brownie mixture in the prepared pan. Scoop large scoops of the cookie dough onto the top of the brownie batter, then sprinkle with the flaky sea salt.
Bake 40-50 minutes, or until a toothpick inserted 1½ inches from the side of the pan comes out clean or with a few moist crumbs. Let cool completely before slicing and serving.