Polychlorinated biphenyls (PCBs) are persistent organic pollutants that are frequently detected in aquatic environments. These compounds accumulate in the fatty tissues of fish, including walleye (Sander vitreus), a popular choice among recreational anglers. Consuming PCB contaminated fish poses significant health risks, including developmental delays, neurological issues, immune system suppression, and potential carcinogenic effects. Although fish consumption advisories provide recommendations for safe intake, they often neglect to address the influence of cooking methods—such as baking, frying, and smoking—on PCB concentrations. This study explores how these cooking methods impact PCB levels in walleye fillets collected from Lake Erie. Fillets from 60 walleye were paired, with one fillet remaining raw while the other underwent one of the three cooking methods before PCB extraction and analysis. The PCB concentrations in raw and cooked fillets were then compared to evaluate the effect of each method on PCB retention. The cooking methods evaluated in this study did not significantly impact the total PCB concentrations in fish fillets compared to raw samples. However, statistically significant increases were observed in the concentrations of specific PCB congeners. This increase is likely due to moisture loss during cooking, which concentrates the PCBs in the remaining tissue. These findings provide critical insights into the influence of cooking methods on PCB exposure, highlighting important considerations for food safety, public health policies, and dietary guidelines to minimize PCB-related health risks.