The aim of this study was to determine the impact of continuous and intermittent aeration on the rate of ammonia removal in the combined nitritation–anammox process. This process was run in two parallel sequencing batch reactors (SBRs), with a working volume V = 10 L, treating sludge digester liquors from the Gdansk (Poland) wastewater treatment plant (WWTP). The ammonia oxidizing bacteria were cultivated from activated sludge from the same plant, whereas the anammox bacteria originated from the Zurich WWTP (Switzerland). Both SBRs were operated with 12-h cycles, temperature 30 °C and hydraulic residence time between 1 and 7 days depending on the operating period. The maximum specific ammonium utilization rate (sAUR) was observed in the reactor with intermittent aeration, and varied in the range of 4.4–4.7 g N kg VSS−1 h−1. The sAUR in the reactor with continuous aeration was slightly lower and ranged from 4.39 to 4.41 g N kg VSS−1 h−1. In the case of intermittent aeration, the additional measurement was performed at two different dissolved oxygen concentrations, i.e., 1 and 0.8 mg O2 L−1, and the observed nitrogen removal rates were 4.7 and 2.7 g N kg VSS−1 h−1 , respectively.