Preheat oven to 375°F and line muffin pan with paper liners or grease cups thoroughly.
Whisk together flour, cocoa powder, pumpkin pie spice, baking soda, and salt in a large bowl.
In a separate bowl, mix pumpkin puree, brown sugar, oil, eggs, and vanilla until smooth.
Pour wet ingredients into dry ingredients and fold gently until just barely combined throughout.
Fold in chocolate chips carefully, reserving some extra for sprinkling on muffin tops.
Fill each muffin cup about three-quarters full using an ice cream scoop for even portions.
Sprinkle remaining chocolate chips on top of each muffin for extra chocolatey goodness.
Bake for 18 to 22 minutes until a toothpick inserted in the center comes out clean.
Cool muffins in the pan for 5 minutes before transferring to a wire cooling rack.
Serve warm or at room temperature and enjoy your delicious fall treat!