Preheat the oven to 350º and spray an aluminum loaf pan with nonstick cooking spray.
In a medium sized bowl mix the cocoa powder, all-purpose flour, and salt together. Pour the dry ingredients through a sifter (or fine mesh strainer) to make sure there are no lumps in the dry ingredients. Set aside.
Next, add melted butter, brown sugar, and peppermint extract to a large bowl and mix together on medium/low with a hand held mixer or stand mixer (using an electric mixer is important).
In a separate small bowl, add the chocolate chips and melt them in the microwave on high for 15 second intervals, stirring and repeating until the chocolate chips are melted. Set aside.
Crack the eggs into the bowl with the butter and sugar mixture and mix on low with a mixer until the eggs are combined.
Add melted chocolate chips to the butter mixture and mix on low until all the ingredients are mixed together.
Slowly add the flour and cocoa powder to the bowl with the chocolate mixture and mix on low until combined.
Pour half of the brownie batter into the greased loaf pan. Then, place 9 thin mint cookies on top of the brownie batter.
Pour the remaining brownie batter over the thin mint cookies. Optionally sprinkle on 2 coarsely chopped Thin Mints on top.
Bake the brownies at 350ºF for 22-25*.
Remove from the oven and sprinkle with flaked sea salt. Let the brownies sit for 10-15 minutes before removing them from the pan.