Preheat the oven to 325 degrees F (165 degrees C).
Whisk flour, cocoa powder, baking soda, and salt together in a bowl. Set aside.
Combine butter and chocolate chips in a microwave-safe bowl. Heat in 30-second intervals, stirring after each interval, until chocolate is melted and creamy. Add eggs one at a time, mixing well to incorporate each one. Add brown sugar, white sugar, and vanilla extract; mix well. Fold in flour mixture until no dry streaks remain. Fold in chocolate chunks.
Drop rounded teaspoonfuls of cookie dough onto a baking stone or nonstick cookie sheets. Sprinkle fleur de sel over the tops.
Bake in the preheated oven until cookies flatten but centers still look soft, 10 to 14 minutes. Transfer to wire racks to cool.
