Preheat the oven to 350 degrees F (175 degrees C). Line cupcake pans with 18 paper liners.

Beat cream cheese and 1 cup sugar in a large bowl until well combined. Add eggs one at a time, mixing well after each addition. Stir in 1 teaspoon vanilla. Spoon batter into the prepared cupcake pans, 2/3 to 3/4 full.

Bake in the preheated oven until golden brown, about 30 minutes. Remove from the oven and cool for 5 to 10 minutes.

Whisk sour cream, remaining 1 cup sugar, and remaining 1 teaspoon vanilla in a medium bowl until smooth. Spoon into the well on the top of each cupcake.

Return to the oven and bake until set, 5 to 7 more minutes. Place the pans on wire racks to cool. Do not remove cupcakes from the pans until completely cool.