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, peanut butter, and vanilla extract until smooth.
Place a layer of graham crackers in the bottom of a greased 8-inch square baking dish. Pour batter over the graham crackers. Bake for 20-25 minutes. Remove from the oven and top with marshmallows. Bake for another 5-10 minutes.