Preheat oven to 350 degrees.
In a large bowl, mix together the flour, brown sugar, cocoa powder, baking soda and salt.
In a smaller bowl, mix together water, applesauce, vinegar and vanilla extract. Pour the smaller liquid ingredients into the larger bowl. Mix to combine.
Stir in chocolate chips. Pour batter mixture into prepared muffin pan. Bake for 18-20 minutes.