Preheat the oven to 325°F (163°C). Line the muffin tin with cupcake liners.
Mix Dry Ingredients: In a medium bowl, whisk together flour, cocoa powder, baking soda, and baking powder.
Mix Wet Ingredients: In a large bowl, using an electric mixer, beat the eggs, sugar, and vanilla extract on high speed until light and fluffy. Reduce speed and blend in the mayonnaise.
Combine: Alternately add dry ingredients and water to the wet mix, starting and ending with the flour mixture. Ensure each addition is well incorporated before adding the next.
Bake: Scoop the batter into the lined muffin tins. Bake for 18 minutes, or until a cake tester comes out clean.
Cool: Let the cupcakes cool in the tin for 10 minutes before transferring them to a wire rack to cool completely