Preheat your oven to 350°F. Line two baking sheets with parchment paper.
In a medium bowl, whisk together the flour, baking powder, baking soda, salt, and cocoa powder. Set aside.
In a large bowl, beat together the granulated sugar, brown sugar, and softened butter until light and fluffy, about 3-4 minutes.
Add the eggs one at a time, mixing well after each addition, then stir in the vanilla extract.
Gradually add the dry ingredients to the wet mixture, alternating with the milk, starting and ending with the dry ingredients. Mix until just combined.
Drop rounded tablespoons of batter onto the prepared baking sheets, spacing them about 2 inches apart.
Bake for 10-12 minutes, or until the tops spring back when lightly pressed. Allow to cool on the baking sheets for 5 minutes before transferring to wire racks to cool completely.
For the filling, beat together the powdered sugar, softened butter, vanilla extract, and milk until smooth and creamy.
Once the whoopie pie cakes are completely cool, spread a generous amount of filling on the flat side of one cake and top with another cake, flat side down. Repeat with remaining cakes and filling.