Preheat oven to 375° F. Line a baking tray with silicone baking mats or parchment paper.
In a mixing bowl, combine brown butter, brown sugar, and sugar. Using an electric hand mixer on medium speed, cream butter and sugars together until light and fluffy.
Add in eggs and vanilla extract and continue to mix on medium speed until fully combined.
In a separate bowl, whisk together flour, baking soda, baking powder, and salt.
Add in dry ingredients and mix on low speed until just combined with the wet ingredients.
Add in chocolate chips. Mix on the lowest speed until combined or fold into the cookie dough until dispersed.
Portion the dough into 2 oz balls. Do not roll the balls.
Place the dough balls onto a baking tray and chill in the refrigerator for at least 1 hour.
Place chilled cookie dough balls on cookie sheet well spaced. I typically do 6 to a pan (2 rows of 3).
Bake in oven for about 12 minutes. Cookies may appear to be slightly underdone.
Remove from oven. Immediately sprinkle with flaky sea salt. Allow cookies to cool on the tray for 2-3 minutes.
Remove cookies from the tray using a spatula and transfer to a wire cooling rack. Allow cookies to cool completely.