Fungi have been shown to be good candidates to remove pharmaceuticals. However, the pilot-scale application mainly deals with the strict growth conditions and competition between microbial communities from wastewater. Thus, the bioaugmentation for removing the pharmaceuticals in municipal wastewater by Trametes versicolor and Aspergillus luchuensis using fluidized bed pelleted bioreactor was studied. To find the optimal performance of bioaugmentation by both fungi periodical biomass volume, 10 and 50 g per 1.25 L bioreactor, were tested. The removal of nutrients, pharmaceutical substances, and changes in the pH value, laccase activity, and total cell number of microorganisms were analyzed. The results showed that bioaugmentation has an effect in removing NH4-N and lower accumulation of NO3-N, whereas PO4−3-P and TOC did not show a significant effect on the reduction of nutrient load compared to the control without fungal addition. The results of removal efficiency for diclofenac, carbamazepine, and sulfamethoxazole showed that there was no significant effect on the removal while the highest removal efficiency (> 90 %) for ibuprofen, ketoprofen, and metoprolol was achieved by both fungi with periodical addition with 50 g of biomass after an incubation time of 3 hours. Finally, the data analysis with AI-based experimental design indicated that A. luchuensis can be a useful fungus for pharmaceutical removal and implies a perspective approach for optimization of fluidized bed pelleted bioreactor. Overall, the obtained results and the use of an AI-based platform is a promising approach for the optimization and operation of fluidized bed pelleted bioreactors.