Make the brownie batter according to the package directions. Stir in the chocolate chips and set aside.
Crush the pretzels in a food processor, or in a heavy-duty plastic bag with a rolling pin, until most are fine but there are still some slightly larger pieces. Combine with the melted butter and press into the prepared pan.
Dollop the brownie batter over the pretzel crust in small portions. Spread the batter over the crust with an offset spatula, being careful not to lift the crust. Bake according to the brownie package directions, adding additional minutes as necessary to cook through.
In the last 5 minutes of cooking, sprinkle the large chunks of pretzel over the top and lightly press in. Continue baking until set.
Remove from the oven and cool completely on a wire rack. Cut into 9 bars.