Preheat oven to 350 degrees. Butter and flour two standard muffin tins, or line muffin tins with paper liners; set aside.
In a medium bowl, whisk together both flours, baking powder, and salt; set aside.
In the bowl of an electric mixer fitted with the paddle attachment, beat butter and sugar until light and fluffy, 3 to 4 minutes, scraping down sides of bowl as necessary. Beat in eggs, one at a time, then beat in vanilla. With the mixer on low, add flour mixture in three parts, alternating with milk and beginning and ending with flour, mixing well after each addition.
Divide batter evenly among muffin cups. Bake, rotating pans halfway through, until golden brown and a cake tester inserted into the center comes out clean, about 20 minutes. Transfer pans to a wire rack to cool for 5 minutes. Remove cupcakes from pan and let cool completely on wire racks before frosting.