1. Preheat the oven to 350 degrees. Line a 12-cup cupcake pan with paper liners.
2. In a medium bowl, whisk together the flour, baking soda, and salt. In a small bowl, stir together the milk, molasses, and vanilla.
3. In the bowl of a stand mixer, beat the butter and brown sugar on medium-high speed until light and fluffy, about 2 to 3 minutes. Reduce the speed to medium-low, add the eggs one at a time, and beat until creamy, 1 to 2 minutes.
4. Slowly add half the flour mixture, then the milk mixture, then the remaining flour mixture, beating until just combined after each addition. (The batter may appear slightly separated; this is okay.)
5. Divide the batter evenly among the liners and bake for about 16-18 minutes until the tops are puffy and a toothpick inserted into the center comes out clean. Remove from the oven and let the cupcakes cool in the pan.
6. While the cupcakes are cooling, in a medium saucepan, heat the butter and brown sugar together over medium heat, stirring until the brown sugar has dissolved, 1 to 2 minutes. Bring the mixture to a boil, then reduce the heat to low and simmer, stirring continuously, for 2 minutes.
7. Add the milk and return to a boil, stirring continuously, until the mixture is well combined, 2 minutes. Remove from the heat and cool to lukewarm, 20 minutes. Transfer mixture to a your stand mixer.
8. With the mixer on low speed, gradually add the powdered sugar. Add additional milk 1 tablespoon at a time if the frosting becomes too stiff (it should be firm but still spreadable).
9. Frost the cooled cupcakes and sprinkle with chopped pecans. Enjoy!