Preheat oven to 350F and line muffin pan with paper liners (12).
Filling: Beat cream cheese until smooth. Add sugar, egg and vanilla; continue beating until smooth. Set aside.
Cupcakes: In a large bowl, sift flour, sugar, cocoa, salt and baking soda together. In another bowl, mix water, oil, vinegar and vanilla. Make a well in the center of dry ingredients and pour in wet mixture; mix until smooth. Pour batter evenly into muffin cups.
Spoon a few tablespoons of the cream cheese filling into the center of each filled muffin cup.