Preheat the oven to 350°F (180°C). Line a 12-cup pan with cupcake paper liners and set aside. Sift the flour, cocoa powder, baking powder, baking soda, and salt into a medium bowl. Set aside.
Using a stand mixer fitted with the whisk attachment or a hand mixer, beat the eggs with sugar and oil until lightened in color, about 3 minutes. Add the vanilla extract. On low speed, add the flour mixture alternately with the milk until the batter is smooth, about 2 minutes. Fold in the chocolate chips.
Fill each paper cup with batter, about 90% full. Bake the cupcakes for 20–25 minutes, or until a cake tester comes out clean. Remove the cupcakes from the pan and let them cool completely on a wire rack. Prepare the ganache.
Use a spatula or piping bag to spread the ganache over the top of the cupcakes. Top with sprinkles, if desired.