Preheat the oven to 350°F (175°C).
In a medium bowl, whisk together the flour, cocoa powder, ginger, cinnamon, baking soda, and salt.
In a large bowl, cream together the softened butter and brown sugar until light and fluffy.
Mix in the molasses and eggs, followed by the vanilla extract until combined.
Gradually add the dry ingredients to the wet mixture, mixing until just combined.
Drop tablespoonfuls of the batter onto a lined baking sheet, leaving space between each to allow for spreading.
Bake for 10-12 minutes, or until the edges are set and the tops are slightly springy.
Allow the cookies to cool completely on a wire rack before filling.
Meanwhile, prepare the filling by beating together the powdered sugar, cream cheese, and milk until smooth.
Sandwich the filling between two cookies, pressing gently to adhere.
Enjoy your gingerbread whoopie pies fresh or store them in an airtight container in the refrigerator.