Preheat the oven to 350°F (175°C). Line a baking sheet with parchment paper.
In a mixing bowl, whisk together the flour, baking soda, baking powder, cinnamon, ginger, nutmeg, and salt. Set aside.
In another bowl, combine the pumpkin puree, granulated sugar, brown sugar, vegetable oil, eggs, and vanilla extract. Use a mixer to beat the mixture until well combined.
Gradually add the dry ingredient mixture to the wet ingredients and mix until just combined. Do not overmix.
Using a cookie scoop or tablespoon, drop rounded tablespoons of dough onto the prepared baking sheet, leaving space between each cookie.
Bake in the preheated oven for 10-12 minutes, or until the cookies are set and a toothpick inserted comes out clean. Allow to cool on the baking sheet for a few minutes before transferring to a cooling rack.
While the cookies are cooling, prepare the filling. In a mixing bowl, beat the softened butter and cream cheese together until creamy. Gradually add the powdered sugar and vanilla extract, mixing until smooth and fluffy.
Once the cookies are completely cooled, spread a generous amount of filling on the flat side of one cookie and sandwich it with another cookie, flat side down. Repeat for the remaining cookies.
Serve and enjoy your delicious Pumpkin Whoopie Pies!