Preheat the oven to 350°F. Lightly grease an 8x8 pan and line with parchment paper.
In a small microwave-safe bowl, melt 1 stick of butter and chocolate chips in 15 second increments while stirring between increments until fully melted. Be cautious to avoid burning the chocolate, it will happen quickly if not stirred completely between intervals.
Melt the remaining 1 stick of butter in a medium-large microwave-safe mixing bowl. Mix in both sugars, then add vanilla extract and eggs.
Fold the melted butter and chocolate chip mixture into the butter and sugar mixture. Mix in flour, salt, and cocoa powder until just combined. Pour batter into the prepared baking pan and spread to smooth the top evenly.
Bake for 40-50 minutes, check them after 40 minutes frequently. The secret to fudgy brownies is to undercook them so that they continue to slightly bake while cooling but not too much. When it's time to take them out of the oven, they'll jiggle ever so slightly in the middle and cooked around the edges. Top with flaky sea salt, if desired.