In a medium bowl, whisk together the flour, cocoa powder, baking soda and salt. Set aside.
In a separate bowl using an electric mixer (or a stand mixer), beat butter, brown sugar and sugar together until light and fluffy, about 2 minutes. Add the egg and vanilla, and mix until combined. Scrape down the sides and bottom of the bowl as necessary.
Add the dry ingredients to the wet ingredients. Beat just until combined and no flour pockets remain.
Use a small cookie scoop to scoop 1 Tablespoon of dough. Roll it into a ball and place on a parchment lined baking sheet. Use your thumb to make an indentation in the center. Repeat with remaining dough, place cookies about 2 inches apart on the baking sheet. Place the baking sheet in the refrigerator for 1 hour.
Ten minutes before taking the dough out of the refrigerator, preheat the oven to 350 F. Bake the cookies for 12 to 14 minutes or until the edges are set (the center will be soft). If the cookies puffed up while baking, use the back of the cookie scoop or a spoon to reinforce the indentation in the center. Transfer cookies to a wire cooling rack to cool completely.
For the ganache, heat the heavy cream until very hot, about 45 seconds in the microwave. Pour over the chocolate chips and let the mixture sit for a minute. Stir the chocolate chips and heavy cream until smooth. If the chocolate isn’t melting, place the bowl in the microwave for 20 seconds on 50% power level.
To assemble the cookies, use a spoon to transfer about 1 teaspoon of chocolate ganache into the thumbprint of every cookie. Place a Mezzetta maraschino cherry (stem removed) on top of the ganache and serve.
Store assembled chocolate cherry thumbprint cookies in an airtight container at room temperature for 2 days. Unassembled cookies will last at room temperature for 5 days.Cookie dough may be stored in an airtight container in the refrigerator for 2 days or in the freezer for 3 months.