Getting Ready: Preheat oven to 350° F. Line a 9x13 baking pan with parchment paper.
Pretzel Crust: Mash pretzels into coarse crumbs. You can do this by putting the pretzels in a ziplock bag and crushing them with a rolling pin, using a mortar and pestle, or pulsing in the food processor.
Pretzel Crust: Mix together pretzels, melted butter, and brown sugar in a large bowl. Firmly press the pretzel mixture into the bottom of the prepared baking pan. Set aside.
Brownies: In a medium-sized bowl, whisk together flour, cocoa powder, and salt. Set aside.
Brownies: In a large mixing bowl, stir melted butter and sugar until well incorporated. Stir in eggs and vanilla. Then fold in the dry ingredients.
Brownies: Evenly distribute spoonfuls of brownie batter on top of the pretzel mixture in the baking pan, and then carefully spread the batter until the pretzels are covered.
Brownies: Bake for 25 to 30 minutes. At 25 minutes, the brownies should be not quite done and still a little gooey in the middle (this is the way I like them). At 30 minutes, they should be mostly cooked through.
Finishing Touches: Sprinkle sea salt on top of the brownies right after they come out of the oven.