Line an 8x8 inch square baking pan with parchment paper, leaving a 2-inch overhang on the sides to facilitate removal.
In a medium mixing bowl, combine the graham cracker crumbs, melted butter, and granulated sugar. Stir until the mixture resembles wet sand.
Transfer the crumb mixture to the prepared pan and press firmly into an even layer using the bottom of a measuring cup.
Place the crust in the refrigerator to chill while preparing the topping.
Place the Nutella and semi-sweet chocolate chips in a heat-proof glass or stainless steel bowl.
In a small saucepan over medium heat, bring the heavy cream to a gentle simmer (do not let it reach a rolling boil).
Pour the hot cream over the Nutella and chocolate chips. Let the mixture sit undisturbed for 2 minutes to allow the chocolate to melt.
Whisk the mixture gently, starting from the center and moving outward, until a smooth and glossy ganache forms.
Pour the fudge mixture over the chilled graham cracker crust and smooth the surface with an offset spatula.
Sprinkle the top evenly with flaky sea salt.
Refrigerate for at least 2 hours, or until the fudge layer is completely set and firm to the touch.
Lift the bars out of the pan using the parchment paper overhang and slice into 16 squares using a warm, sharp knife.