Kraft mill effluent, due to its organic matter content and acute toxicity, must be treated. A primary treatment followed by a secondary treatment is the most common system. Aerated lagoon is also considered an effective biological treatment, although this technology has some drawbacks related with operation parameters and land extension space. Moreover, the recovery efficiency for micropollutants contained in kraft mill effluent is questioned due to the anoxic zone in the system. The goal of this work is to evaluate the performance of the aerated lagoon to remove stigmasterol contained in kraft mill effluents. Kraft mill effluent was treated by an aerated lagoon (AL), which was operated with three different stigmasterol load rates (SLR = 0.2, 0.6 and 1.1 mg/L x d) and a hydraulic retention time of 1 day. The AL’s maximum Chemical Oxygen Demand (COD) removal was 65%, whereas the Biological Oxygen Demand (BOD5) was around 95%. The removal efficiency of stigmasterol removal was 96% when SLR 1.1 mg/L x d, although an accumulation of stigmasterol was detected for lower SLR.