Preheat your oven to 350°F (175°C) and line a muffin tin with cupcake liners.
In a mixing bowl, combine flour, baking soda, baking powder, cinnamon, nutmeg, ginger, and salt. Whisk until blended.
In another bowl, blend together the pumpkin puree, sugar, vegetable oil, and eggs until smooth.
Gradually add the dry ingredients to the wet ingredients, stirring until just combined.
Fill the cupcake liners about two-thirds full with the batter. Bake for 20 minutes or until a toothpick inserted into the center comes out clean.
Allow cupcakes to cool in the tin for 5 minutes before transferring them to a cooling rack to cool completely.
For the cream filling, beat together the softened cream cheese, powdered sugar, and vanilla extract until smooth.
Once the cupcakes are completely cool, use a piping bag or a knife to cut a small hole in the center of each cupcake and fill it with the cream cheese filling.
To make the frosting, beat the softened butter until creamy. Gradually mix in powdered sugar and milk until you reach the desired consistency. Add vanilla extract and beat until fluffy.
Frost the filled cupcakes generously with the frosting. Optionally, sprinkle a little cinnamon on top.