Preheat oven to 350°.
Drain the cherries, reserving the juice.
In a mixing bowl, beat the butter and sugar. Add egg and vanilla. Mix well. Add flour, cocoa powder, baking soda, baking powder, and salt. Mix well.
Roll the dough into 1 inch balls (like large marbles). Place on a parchment-paper-lined baking sheet. Press your thumb into the dough to create an impression. Place a cherry in the center of each cookie. Set aside.
In a small saucepan, combine chocolate chips and sweetened condensed milk. Cook and stir constantly over low heat until the chocolate is melted. Stir in 4 teaspoons reserved cherry juice. Spoon this mixture over the cherries; spread to cover.
Bake the cookies for 10 minutes, until the edges are cracking. Cool.