Preheat the oven to 350 F. In a large bowl, whisk together flour, sugar, cocoa powder, salt, and baking soda. Add in the eggs, melted butter, and vanilla extract until smooth.
Evenly pour half of the brownie batter into a greased 8-inch square baking dish. Place the Reese's peanut butter cups on the batter. Cover with the remaining brownie batter. Bake for 20-25 minutes.