Pharmaceutical waste has attracted significant attention in the past two decades due to the current high consumption of pharmaceuticals together with the development of reliable detection technologies. In order to acquire better understanding on pharmaceuticals removal in biological processes, the treatment of synthetic wastewater containing diclofenac (DFN) and ibuprofen (IBU), two of the most commonly prescribed medicines worldwide, was studied using a moving bed biofilm reactor (MBBR). An 8.5-L aerobic MBBR with Kaldnes packing filling ratio of 40% was designed. The controlled parameters were pH within neutral range, temperature of 37 °C, mixed liquor suspended solids (MLSS) of 2100 mg/L, and attached growth equal to 1300 mg/L. Tests were conducted for four different initial pharmaceuticals concentrations: 2, 4, 7 and 10 mg/L, two hydraulic retention times (HRT): 5 and 10 h and two chemical oxygen demands (COD): 500 and 1000 mg/L. Results demonstrated that generally, DFN had higher removal percentage than IBU in the MBBR. At HRT = 10 h, DFN removal was between 30.83 and 66.01%, while it was 11.33 and 37.33% for IBU. At HRT = 5 h, DFN and IBU removal were respectively between 31.10–65.33 and 0–35.10%. It can be concluded that HRT = 5 h is the optimal time for DFN, while 10 h HRT promises noticeably better IBU removal. Furthermore, results revealed that DFN is better removed in the lower COD, while IBU showed better removal in the higher COD. Finally, the study on their toxicity reveals that pharmaceuticals exert slightly negative effect on COD removal.