Preheat oven to 350 degrees F (175 degrees C). Line 12 muffin cups with paper liners.
Mix brownie mix, oil, eggs, and water together in a bowl until well combined. Mix cream cheese, sugar, butter, flour, and vanilla extract together in a separate bowl.
Fill each muffin cup 1/2-full with brownie mix; top with cream cheese mixture. Spoon brownie mix over cream cheese mixture layer.
Bake in the preheated oven until a toothpick inserted in the center of the brownie part comes out clean, 20 to 25 minutes.
Not all the brownies will be used in the cupcakes. The nutrition data for this recipe includes the full amount for the brownies. The actual amount of brownies consumed will vary.
The directions given for the brownie mix are according to the Pillsbury(R) mix. Follow directions on brownie box if using a different brand.
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