Heat oven to 400 degrees F. Line 6 jumbo muffin cups with paper liners.
Mix the flour, cocoa powder, baking soda, baking powder and salt together in a bowl.Stir the brown sugar around in a second bowl and mash out any lumps. Stir in the pumpkin, eggs, milk, and vanilla and mix well.
Pour the dry mixture into the pumpkin mixture and stir a few strokes, then pour the melted butter in and stir (never over-beat muffin batter) until blended.Stir in the chocolate chips. Reduce oven heat to 375 degrees F. Divide batter equally among muffin cups and bake for 23-26 minutes or until a toothpick or chopstick inserted in center comes out clean.