Preheat your oven to 350ºF and grease an aluminum loaf pan with nonstick cooking spray.
In a medium bowl, combine cocoa powder, all-purpose flour, and salt. Sift the dry ingredients to remove any lumps. Set aside.
In a large bowl, mix melted butter, brown sugar, and peppermint extract using an electric hand mixer on medium/low speed.
In a small bowl, melt the chocolate chips in the microwave in 15-second intervals until smooth. Set aside.
Crack the eggs into the bowl with the butter and sugar mixture. Mix on low speed until well combined.
Add the melted chocolate chips to the butter mixture and mix on low until fully incorporated.
Gradually add the flour and cocoa powder mixture to the chocolate mixture. Mix on low until combined.
Pour half of the brownie batter into the greased loaf pan. Arrange 9 Thin Mint cookies on top of the batter.
Pour the remaining batter over the cookies. Optionally, sprinkle 2 coarsely chopped Thin Mints on top.
Bake the brownies at 350ºF for 22-25 minutes*.
Remove from the oven and sprinkle with flaked sea salt. Let the brownies cool in the pan for 10-15 minutes before removing them.