Preheat oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease it. In a large bowl, whisk together flour, sugar, cocoa powder, baking powder, baking soda, and salt.
In another bowl, beat together eggs, milk, vegetable oil, and vanilla extract until smooth and well combined.
Pour wet ingredients into dry ingredients and gently fold with a spatula until just combined. Avoid overmixing to keep muffins tender. Fold in chocolate chips, reserving a few for topping.
Divide batter evenly among the 12 muffin cups, filling each about 2/3 full. Sprinkle reserved chocolate chips on top.
Bake for 20–25 minutes, or until a toothpick inserted in the center comes out clean. Cool in the pan for 5 minutes, then transfer to a wire rack.