Step 1

Position a rack in the center of the oven and preheat to 350 degrees F. Line a 12-cup muffin tin with liners. Beat together the cream cheese, egg, 1/3 cup of the granulated sugar and 1/2 teaspoon of the vanilla extract in a medium bowl on medium speed with an electric mixer until smooth and no lumps remain, 1 to 2 minutes. Set aside.

Step 2

Whisk the flour, cocoa powder, brown sugar, baking soda, salt and remaining 2/3 cup granulated sugar in a large bowl. Add the oil, the remaining teaspoon vanilla extract and 1 cup water and mix until combined. Let the batter rest 10 minutes at room temperature, then stir in the vinegar.

Step 3

Divide the chocolate batter evenly among the prepared muffin cups, filling each cup about two-thirds full. Drop about 2 tablespoons of the cream cheese filling in the center of each cupcake.

Step 4

Bake until the cream cheese filling has set and a toothpick inserted into the chocolate cupcake comes out clean, about 20 minutes.

Step 5

Cool in the tin 5 minutes and then use a butter knife or small offset spatula to carefully remove the cupcakes to a wire rack. Cool the cupcakes completely before serving, about 30 minutes.