In a medium bowl, whisk together the gluten-free flour, cocoa powder, baking soda and salt.
In the bowl of a stand mixer, or using a hand mixer, cream together the butter and granulated sugar until light and fluffy, about 2-3 minutes.
Add the eggs and vanilla extract and mix until well combined, scraping down the bottom and sides of the bowl halfway through.
Add the dry ingredients and mix on low until just combined.
Cover the dough and refrigerate for at least 1 hour, or up to 3 days.
Preheat the oven to 350°F. Line large baking sheets with parchment paper or silicone baking mats.
Scoop the cookie dough into round balls, 1½ tablespoons per ball. Place on the prepared baking sheet, about 3 inches apart, and flatten slightly.
Bake for 8 minutes, then remove from the oven and immediately top each cookie with a marshmallow.
Return the pan to the oven and bake for an additional 2 minutes. Remove the cookies from the oven and use your fingers to flatten the marshmallows a little.
Let cool on the baking sheet for 5 minutes. Transfer to a wire rack to cool completely.
For the ganache: Place the semi-sweet chocolate in a bowl. Microwave the heavy cream until simmering, about 1 minute. Pour the hot heavy cream over the chocolate and let sit for 30 seconds. Mix until smooth. If the chocolate still isn’t melted, microwave the ganache for 20-second increments at 50% power, stirring after each increment until completely melted and smooth.
Spoon melted chocolate over each cooled marshmallow-topped cookie. Enjoy!