Preheat oven to 350 degrees F (175 degrees C). Line one 12-cup muffin pan with paper liners.

Stir together flour, cocoa powder, baking powder, baking soda, and salt in a bowl.

Beat together butter, white sugar, and brown sugar in a large bowl with an electric mixer a medium speed until light and fluffy, about 90 seconds. Add eggs, one at a time, beating until just combined after each addition. Beat in vanilla.

Beat in flour mixture one-third at a time, alternating with 1/4 cup milk, on low speed until just combined. Fill each prepared muffin cup with 1/4 cup batter

Bake until a toothpick inserted in centers comes out clean, about 20 minutes. Cool in pan on a wire rack 5 minutes. Transfer to wire rack to cool completely, about 20 minutes.

Meanwhile, beat together cream cheese and butter in a large bowl with an electric mixer at medium-high speed until light and fluffy, about 30 seconds. Reduce speed to low; add powdered sugar, 1 cup at a time, beating until frosting is smooth.

Fit a piping bag with a large star or round tip and fill with frosting. Pipe frosting onto cupcakes. Garnish with pomegranate arils. Serve immediately or store, chilled, in an airtight container up to 1 week.