Preheat the oven to 350°F. Line two large baking sheets with parchment paper or use a silicone baking mat. Set aside.
In a large mixing bowl, whisk together pumpkin puree, light brown sugar, vegetable oil, eggs, and vanilla extract until all ingredients are well incorporated.
In a separate bowl, whisk together the dry ingredients: all-purpose flour, baking powder, baking soda, salt, cinnamon, ginger, and nutmeg. Add to the wet mixture. Stir gently using a rubber spatula until just combined and no big lumps of flour remain. Don’t overmix.
Scoop the batter using an ice-cream scoop onto the prepared baking sheet or silicone mat, leaving about 1 inch to 2 inches between each cookie.
Bake in the preheated oven for 10-12 minutes or until the cookies are puffed out, dry on top, and set. Remove from the oven and let cool for 5 minutes. Then, transfer to a cooling rack.
While the cookies are cooling, prepare the cream cheese filling. In a mixing bowl whisk together the softened cream cheese, softened butter, and vanilla extract until creamy and smooth, about 1-2 minutes. The butter and cream cheese should be at room temperature for easy mixing. Then, whisk in the powdered sugar and salt until all ingredients are incorporated well. Scrape the bottom and the sides of the bowl. Transfer the cream cheese filling to a piping bag or a ziplock bag with a corner cut out.
When the cookies are cooled, assemble the pumpkin whoopie pies by piping the filling on the flat side of the cookie and top with the other cookie to make a sandwich. Repeat with the remaining cookies. Chill the pumpkin whoopie pies in the refrigerator for about 30-60 minutes. Enjoy!