Palm oil mill effluent (POME) is a high-strength wastewater which is rich in nutrients, organic matter and suspended solids. Discharging POME without adequate treatment into the environment can cause undesirable hazards to both humans and the environment. Conventional treatment methods, such as ponding systems and anaerobic digestion, are widely applied but face several limitations in managing POME, including inconsistent removal efficiency, extended treatment duration, extensive land use and unfavourable weather conditions. In contrast, fungal-based treatment systems are gaining interest due to the ability of the fungi to produce a wide range of extracellular enzymes, degrade complex organic or recalcitrant pollutants and possess remarkable adaptability to harsh environmental conditions. This review highlights the advantages of the fungal-based treatment systems over conventional treatment methods. It also focuses on the potential of diverse fungal strains as emerging pollution control for POME treatment, as well as in understanding fungal pollutant removal mechanisms and operational factors that influence fungal-based treatment performance. Finally, the review identifies the implementation challenges and future research directions, providing a comprehensive perspective on fungal-based POME treatment as a sustainable and scalable technology for pollution control.