Pharmaceutically active compounds (PhACs) in wastewater pose significant environmental risks due to their persistence and potential to disrupt aquatic ecosystems. Onsite wastewater treatment systems (OWTS) often fail to adequately remove PhACs. This study investigated the efficiency of a multi-module biochar filter (MmBF) system as secondary treatment in OWTS for removing PhACs. Two parallel MmBF systems, each comprising six sequential modules filled with biochar, were evaluated for their removal of 25 detected PhACs across multiple pharmaceutical classes. The MmBFs were operated with municipal wastewater as influent for over one year, after which wastewater samples were collected and analysed from the influent and effluent of each module. The MmBFs showed consistent reduction in the aggregated PhACs concentrations by >99% over several sampling occasions, with only six PhACs having less than 95% removal. The first aerobic module M1 contributed to more than 92% of the total removal. The subsequent aerobic modules (M2-M3) provided additional reduction, resulting in over 98% of PhACs removal in the aerobic modules. In contrast, the anoxic modules (M4-M5) had a lower overall contribution, but the removal of specific compounds was observed, suggesting potential anaerobic degradation. This study demonstrates the potential of biochar-based systems as a sustainable option for OWTSs.