Preheat the oven to 375. Line a muffin pan with paper liners and set aside.
Combine the cherries and the brown sugar in a small pan and simmer for about 5-7 minutes. Let cool while you make the batter.
Using a stand mixer beat the softened butter with the granulated sugar until light and creamy.
Add the eggs one at a time scraping down after each one then add the vanilla.
In a bowl whisk together the flour and baking powder.
Gradually add some of the flour and the milk alternately until all of both have been added. Scrape down and mix on low until smooth.
Fold the cherries into the muffin batter along with the chocolate chunks.
Divide the batter evenly between the 12 muffin liners.
Bake in the oven for 30-35 minutes or until golden brown on top and they spring back when gently pushed with your finger.