Heat the oven to 350 degrees and line a baking sheet with parchment paper.
Stir the flour, ginger, cinnamon, baking soda, and salt together in a bowl.
Beat the butter and brown sugar until creamy, then mix in the molasses and egg yolk.
Add the dry ingredients to the butter mixture and stir until a soft dough forms.
In a separate bowl, combine the cream cheese, pumpkin puree, and granulated sugar until smooth.
Divide the dough into eight equal pieces. Flatten each piece, place a spoonful of filling in the center, and seal the dough around it.
Shape each stuffed ball into a round cookie and press lightly to create a pumpkin-like form with simple face indentations on top.
Place the cookies on the baking sheet and bake for 12 to 14 minutes until the edges are set.
Let the cookies cool on the sheet for 5 minutes before moving them to a rack.