Preheat the oven to 350° and line cupcake pan with papers.
In a medium bowl: add sifted cocoa powder and dark brown sugar. Pour in the boiling water and whisk until combined. Set aside.
Within a large bowl: beat the butter and granulated sugar together, about 2 minutes until light and fluffy. Set aside.
In a small bowl: mix flour, baking powder, baking soda, and salt. Set aside.
In the large bowl with sugar and butter: add vanilla and 1 egg, mix well. Add 1/3 of the flour mixture and mix until combined. Then add 2nd egg, mix well. Finally, add the remaining flour mixture and beat until combined. Use a spatula as necessary to scrape sides of the bowl.
Add the chocolate mixture to the batter and beat until combined (about 30 seconds).
Scoop about 1/3 cup of mixture into each cupcake liner and place cupcake pan on the center rack in the oven.
Bake for about 20-25 minutes, until a toothpick inserted in the middle of the cake comes out clean. While cupcakes are baking, make frosting.
Let cupcakes sit for 5 minutes in the pan and place on cooling rack.