Preheat the oven to 350°F and line a muffin pan with baking cups.
In a medium bowl, stir together the flour, cocoa powder, baking soda, baking powder and salt. Set the mixture aside.
In the bowl of a stand mixer fitted with the paddle attachment, cream together the butter with the sugar until light and fluffy, about 2 minutes. Add the eggs, one at a time, beating until combined and scraping down the side of the bowl as needed. Beat in the vanilla then alternately beat in the flour mixture and the milk, starting and ending with the flour mixture.
Scoop the batter into the baking cups then bake for 18 to 22 minutes until a toothpick inserted comes out clean. Remove the cupcakes from the oven and transfer them to a cooling rack to cool completely.
While the cupcakes cool, make the cupcake toppers by melting the candy melts according to package directions. Transfer the mixture to a piping bag. Place the pretzel sticks on a wax paper-lined baking sheet, spacing them 2 to 3 inches apart. Pipe the candy melts over the pretzel sticks in the shape of a tree then immediately top the trees with the sprinkles. Transfer the baking sheet to the fridge for 10 minutes until the trees have fully hardened.