Preheat oven to 350 degrees, line muffin tin with wrappers, set aside. In a large bowl, add the flour, sugar, baking powder, baking soda, and salt. Whisk to combine. Set aside.
In a medium-sized bowl, add in the remaining ingredients. Stir to combine, add the wet mixture to the dry and stir until just combined and no dry spots. Divide the batter among the 12 cupcakes wrappers, about 2/3 of the way full. Bake for 17-19 minutes, until a toothpick inserted comes out mostly clean. Place on a wire rack for 5 minutes, take out and place directly on the rack to cool completely.
Brown Sugar Frosting
In a small saucepan, whisk the flour into the milk and cook over medium heat, whisking continuously until thick. Remove from heat, stir in the vanilla and let cool to room temp.
With a hand mixer or stand mixer, cream the butter and sugar until light and fluffy and there is no graininess left. Add in the cooled milk mixture and beat it on high speed until a whipped cream consistency. This can take a while, do not give up! Well worth the effort. Frosting cupcakes and enjoy! Any leftover cupcakes should be refrigerated.