Preheat your oven to 350°F (175°C) and prepare your muffin tin.
In a large mixing bowl, whisk together the dry ingredients: gluten-free flour, pumpkin pie spice, baking powder, baking soda, and salt.
In another bowl, mix the granulated sugar, brown sugar, pumpkin puree, vegetable oil, eggs, and vanilla extract until smooth.
Gradually add the dry ingredients to the wet mixture and stir gently until just combined.
In a separate bowl, beat the cream cheese, powdered sugar, and vanilla extract until smooth and creamy.
Fill each muffin cup halfway with pumpkin batter, add a spoonful of cream cheese filling, and cover with more pumpkin batter until ¾ full.
Bake for 18-22 minutes, checking for doneness with a toothpick.
Allow muffins to cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.