Preheat your oven to 350°F (175°C) and line two standard muffin tins with 18 paper liners.
In a medium mixing bowl, whisk together the all-purpose flour, baking soda, baking powder, pumpkin pie spice, and salt until thoroughly combined.
In a separate large mixing bowl, whisk the eggs, light brown sugar, and granulated sugar together until the mixture is smooth and the sugars have begun to dissolve.
Add the vegetable oil, pumpkin puree, and 2 teaspoons of alcohol-free vanilla extract to the egg mixture, whisking until the wet ingredients are fully emulsified.
Gradually add the dry ingredient mixture into the wet ingredients, using a rubber spatula to gently fold the batter just until no streaks of flour remain. Be careful not to overmix to ensure a light texture.
Divide the batter evenly among the 18 prepared cupcake liners, filling each approximately 3/4 full.
Bake for 18 to 22 minutes, or until a toothpick inserted into the center of a cupcake comes out clean and the tops spring back when lightly touched.
Allow the cupcakes to cool in the pan for 5 minutes, then transfer them to a wire rack to cool completely to room temperature before frosting.
Prepare the frosting by beating the room-temperature cream cheese and softened butter together in a clean bowl until the mixture is completely smooth and free of lumps.
Add the powdered sugar one cup at a time, beating on low speed until incorporated, then add the remaining 1 teaspoon of alcohol-free vanilla extract.
Increase the mixer speed to high and beat the frosting for 2 minutes until it is light, fluffy, and holds its shape.
Pipe or spread the cream cheese frosting onto the cooled cupcakes and serve at room temperature.