Preheat the oven to 350F (177C). Line two baking sheets with parchment paper.
In a large bowl, whisk together gluten-free flour blend, cocoa powder, baking soda, and salt. Set aside.
Cream together butter, granulated sugar, and brown sugar with an electric mixer until light and fluffy, about 2-3 minutes.
Add in eggs and vanilla extract. Mix until combined.
Add in dry ingredients, a little bit at a time, and mix until just combined. Stir in the chocolate chunks, reserving ½ cup of chocolate chunks for later.
Scoop out the dough into 2.5 tablespoon sized balls and place on the prepared baking sheets, leaving at least 2 inches between each ball.
Top the dough balls with the remaining chocolate chunks.
Bake at 350F for 10-12 minutes, until edges are set. Remove from the oven and immediately sprinkle the tops of the cookies with flaky sea salt. Allow the cookies to cool for 5 minutes on the pan before placing on a cooling rack to finish cooling.