Food intake is one of the principal exposure routes of polybrominated diphenyl ethers (PBDEs) in humans. This study focuses on fish consumption as a PBDE exposure route. A probabilistic intake assessment of PBDEs and healthy long chain omega-3 PUFAs (LC n-3 PUFAs) was conducted for Belgian fish consumers in order to study the balance of the intake of LC n-3 PUFAs and PBDEs. Based on the observed fish consumption level in the sample, the mean intake of brominated diphenyl ether (BDE)-28, 47, 99, 100, 153, and 154 via fish was 0.85 ng/kg body weight (bw)/day and the intake of LC n-3 PUFAs was 3.45 mg/kg bw/day, being low compared to the recommendations. Scenario analyses showed that consuming 150 g salmon twice a week is advisable to achieve the recommended LC n-3 PUFA intake with a rather low PBDE intake. When replacing 150 g salmon by herring, the PBDE intake is higher without an increase in LC n-3 PUFAs. In contrast, the combination of cod and salmon leads to a similar PBDE intake compared to twice a week salmon, but to a lower LC n-3 PUFA intake. In conclusion, the methodology presented in the paper allows balancing benefits and risks related to fish consumption.