Preheat the oven to 350°F (175°C) and line two baking sheets with parchment paper.
In a medium bowl, whisk together flour, baking powder, baking soda, cinnamon, ginger, nutmeg, and salt.
In a large bowl, whisk together vegetable oil, brown sugar, pumpkin puree, egg, and vanilla until smooth.
Gradually stir the dry ingredients into the wet ingredients until fully combined.
Using a cookie scoop or spoon, drop rounded tablespoons of batter onto prepared baking sheets, spacing them about 2 inches apart.
Bake for 10-12 minutes or until the tops spring back when lightly touched. Let cool on the baking sheets for 5 minutes, then transfer to a wire rack to cool completely.
Meanwhile, make the filling. In a medium bowl, beat together the cream cheese and butter until smooth. Add powdered sugar and vanilla, and beat until fluffy and fully combined.
Assemble the whoopie pies. Spread or pipe a generous amount of filling onto the flat side of one cookie and sandwich with another.
Chill the assembled whoopie pies in the fridge for 20 minutes to firm up the filling before serving.