Preheat your oven to 350°F (175°C). Line a muffin tin with paper liners.
In a large mixing bowl, whisk together the gluten-free flour, cocoa powder, sugar, baking powder, baking soda, and salt.
In another bowl, beat the eggs, then add the milk, vegetable oil, and vanilla extract. Mix well.
Pour the wet ingredients into the dry ingredients and stir until just combined. Fold in the chocolate chips.
Divide the batter evenly among the muffin cups, filling each about ⅔ full.
Bake for 18-20 minutes, or until a toothpick inserted into the center comes out clean.
Let the muffins cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.