Preheat oven to 350°F. Line 2 large baking pans with parchment or a silicone baking mat. Set aside.
In a medium-size mixing bowl, use a whisk to sift together flour, pumpkin pie spice, baking powder, baking soda and salt.
In a separate mixing bowl use an electric mixer to cream together butter, granulated sugar and brown sugar with vanilla extract. Beat on medium-high speed for 2-3 minutes until fluffy.
Add the eggs one at a time, beating well after each addition. Add canned pumpkin puree, mix to combine.
Lower the speed of the mixer and gradually add the dry ingredients. Stop and scrape the sides of the bowl as needed. Beat until fully moistened.
Using a 2 Tbsp or a small ice cream scoop to divide the dough onto the sheet pans. Leave at least 2-inches between to allow for spreading. Bake for 10 minutes. Cool on pan for 5 minutes then remove to a cooling rack to cool completely.
Filling: Using an electric mixer, beat together cream cheese, butter and vanilla on medium-high speed until combined. Lower the speed of the mixer and gradually add powdered sugar. Beat in marshmallow fluff at the end, just until smooth.
Divide cream cheese filling between whoopie pies and sandwich together. (You can use an icing spatula or a piping bag to pipe the filling.)
Store in an airtight container chilled for up to 1 week. Place wax paper between if stacking.