To make the brown butter, melt 1/2 cup of unsalted butter in a pan over medium heat for about 5 minutes, until the butter foams and little brown specks appear. Be careful not to let it burn! Once the butter turns an amber color and has a nutty aroma, remove it from the heat and stir in 2 teaspoons of water or milk (to make up for the loss of moisture) to the brown butter. Transfer it to a small bowl to cool to room temperature.
In a bowl or stand mixer, cream together the room temperature brown butter with the sugars for a few minutes. Add egg and vanilla. Mix until well combined.
Add flour, baking soda, and salt. Mix until just combined. Careful NOT to over mix or you may end up with flat cookies. Fold in chocolate chips and crushed mini pretzels.
Using a medium cookie scoop, form cookie doughs into balls (1 1/2 tablespoons size). Place the cookie dough balls on a baking sheet and freeze the dough balls for 20 minutes.
Preheat oven to 350ºF. Line a baking sheet with parchment paper and place dough balls on the baking sheet. Bake for about 10-11 minutes. Remove from oven, sprinkle with flaky sea salt. It's ok if they are a little undercooked, they will continue to bake as they cool. Enjoy!