Preheat oven to 350 degrees F (175 degrees C). Line 12 muffin cups with foil cupcake liners.

Place a vanilla wafer cookie into the bottom of each cupcake liner.

Beat cream cheese, sugar, eggs, and vanilla extract together in a bowl until smooth; pour atop the cookies until the liners are about 3/4 full.

Bake in preheated oven until center is nearly set and slightly collapsed, about 20 minutes.

Refrigerate cupcakes 2 hours to overnight. Spoon cherry pie filling onto the cupcakes.