Preheat the oven to 350 degrees Fahrenheit. Line a baking sheet with parchment paper.
Place the cubed butter in a small saucepan and melt on medium-low heat until it turns a golden-brown color and has a nutty smell, about 5-7 minutes. It will foam up during this time so keep stirring and checking the color under the foam. Once it starts to turn color, don't walk away as it can burn quickly. Let the butter cool for 20-30 minutes.
Using a hand or stand mixer, mix together the cooled brown butter, brown sugar and granulated sugar until combined. Add the eggs and vanilla and mix until combined.
In a separate bowl, combine the flour, baking soda and salt. Add the dry ingredients to the butter mixture and mix on low until most of the flour is combined. Don't overmix! Add the chocolate chips and pecans and mix on low until incorporated.
Using a cookie scoop or small ice cream scoop, scoop about 3 tablespoons of cookie dough into mounds and place onto the cookie sheet at least 2 inches apart.
Bake for about 12 minutes until the cookies are beginning to turn golden brown. It is better to underbake than overbake! Sprinkle each cookie with sea salt as soon as they come out of the oven. Let cool for a few minutes on the baking tray and then transfer to a cooling rack to cool completely.