Unused pharmaceutical compounds (PhCs) discharged into the aquatic environment have been regarded as emerging pollutants due to potential harmful effects on humans and the environment. Microbial bioremediation is considered as a viable option for their removal from wastewater. The aim of this study was to assess the simultaneous removal of carbamazepine (CBZ), diclofenac (DCF) and ibuprofen (IBP) by previously isolated fungi (Aspergillus niger, Mucor circinelloides, Trichoderma longibrachiatum, Trametes polyzona, and Rhizopus microsporus). The tolerance to PhCs was conducted by tracking the fungal mycelium mat diameters in solid media and its dry biomass in liquid media, at the drug concentration range of 0.1 to 15 mg/L. The fungal enzymatic activities were determined for lignin peroxidase (LiP), manganese peroxidase (MnP) and laccase (Lac), respectively. The PhC removal efficiency of the fungi was assessed in aerated batch flasks and the drug concentrations and intermediate compounds formation were determined by using SPE-UPLC/MS. A tolerance over 70% was recorded for all the fungi at drug concentration of 0.1 mg/L. Manganese peroxidase was produced by all the fungi with very low amount of LiP, while all the enzymes were produced by T. polyzona. The pH of 4.3, temperature 37 ± 1.5°C and incubation time of 6 days were the optimum parameters for the fungal enzymatic activities. The best removal of CBZ (87%) was achieved by R. microsporus after 10 days. Between 78 and 100% removal of DCF was observed by all the fungi after 24 h, while 98% of IBP was removed after 2 days by M. circinelloides. Only a few intermediate compounds were identified after 3 days and disappeared after 10 days of incubation. This study demonstrated that apart from the basidiomycetes, the ascomycetes and zygomycetes are also producers of ligninolytic enzymes and have the ability to biodegrade emerging pollutants such as PhCs.