Preheat the oven to 350. Line a cupcake tin with paper liners, then set aside.
In a large bowl, whisk together the flour, brown sugar, baking powder, cinnamon, pumpkin pie spice, and salt. In a small bowl or measuring cup, whisk together the pumpkin, milk, oil, egg, and vanilla. Pour the wet ingredients into the dry ingredients, and mix until just combined.
Scoop the muffin batter into the prepared cups, filling 3/4 full. Sprinkle with cinnamon sugar, then top with pumpkin seeds.
Bake 15-17 minutes, until a toothpick inserted in the center comes out clean.