Preheat your oven according to the temperature specified on the brownie mix package for a 13x9 inch pan. Grease a 13x9 inch baking pan to prevent sticking. This sets you up to work efficiently as you move through the recipe.
In a small saucepan, whisk together the granulated sugar, light corn syrup, eggs, unsalted butter, and vanilla extract. Place the saucepan over medium-high heat. Cook, stirring continuously, until the mixture thickens enough to coat your spoon, about 15 minutes. I always make sure to stir constantly so the eggs don’t scramble and the filling stays smooth.
Mix the brownie batter according to the package instructions, making sure to incorporate any additional ingredients the box requires. Pour the batter into the prepared 13x9 inch baking pan. Bake in the preheated oven for 20 minutes to partially set the brownies.
Once the filling in the saucepan has thickened (about 15 minutes total), stir in the coarsely chopped pecans. Continue to cook, stirring, for 2-3 minutes more, until the mixture is the consistency of runny oatmeal—loose enough to pour but not watery.
Remove the pre-baked brownies from the oven. Immediately pour the cooked pecan pie filling (with pecans from Step 4) over the brownie layer, spreading it evenly to cover the surface. Return the pan to the oven and bake for an additional 25-30 minutes, or until the filling only jiggles slightly in the center when you move the pan. For a richer flavor, I sometimes sprinkle a little sea salt over the top right before the final bake.
Remove the pan from the oven and let the brownies cool completely to room temperature before cutting into bars. This helps the filling set properly and ensures clean cuts for serving.