Preheat the oven to 350°F. Grease a muffin tin or line it with paper liners.
In a medium bowl, whisk together the flour, baking soda, and salt. Set aside.
In a large bowl, cream together the softened butter, brown sugar, and granulated sugar until light and fluffy. Add the egg and vanilla extract, mixing until well combined.
Gradually add the dry ingredients to the wet ingredients, mixing until just combined. Fold in the graham cracker crumbs and chocolate chips.
Scoop about 2 tablespoons of the cookie dough into each muffin cup, pressing down slightly to form a cup shape.
Bake for 10-12 minutes or until the edges are golden brown. Remove from the oven and immediately press a few mini marshmallows into the center of each cookie cup.
Return to the oven for an additional 2-3 minutes, until the marshmallows are puffed and slightly golden.
Allow the cookie cups to cool in the pan for 5 minutes before transferring to a wire rack to cool completely.
These cookie cups can be served warm or at room temperature.