Conventional and single-stage anaerobic ammonium oxidation (ANAMMOX) was carried out in bench-scale reactors to treat chlortetracycline (CTC) wastewater. The total nitrogen (TN) removal efficiency and rate for conventional ANAMMOX was 66.6 ± 5.9% and 2.7 ± 0.2 kg N/(m3·d), respectively, which was 58.6 ± 3.8% and 1.2 ± 0.1 kg N/(m3·d) for single-stage ANAMMOX. Single-stage ANAMMOX showed higher tolerance to CTC than conventional ANAMMOX. The nitrogen removal of conventional and single-stage ANAMMOX began to deteriorate when CTC was added, to 40 and 80 mg/L, respectively, with the former totally inhibited at 120 mg/L CTC and the latter at 140 mg/L CTC. TN removal rates were recovered to 1.2 and 0.7 kg N/(m3·d), respectively, when CTC concentration was reduced to 20 mg/L for 8 days. This study implied that ANAMMOX could be efficiently used to treat pharmaceutical wastewater, with single-stage implementation being more stable under antibiotic pressure.