Prep the oven. Preheat the oven to 375°F (190°C) and line two 12-cup muffin tins with cupcake liners.
Mix the dry ingredients. In a large mixing bowl or the bowl of a stand mixer, sift together the flour, sugar, cocoa powder, baking soda, and salt.
Add the wet ingredients. Add eggs, milk, vegetable oil, water, and vanilla extract to the dry ingredients. Beat at low speed for 30 seconds, then increase the speed to medium and beat until the mixture is smooth and fully combined (about 2 minutes). Then, scrape down the sides of the bowl as needed.
Fill the cupcake liners. Fill the prepared cupcake liners ¾ full with the batter.
Bake. Bake for 17–20 minutes, rotating the pans halfway through for even baking. The cupcakes are done when a toothpick inserted into the center comes clean.
Cool. Remove cupcakes from the tins and transfer them to a wire rack to cool completely before adding the filling.