There are certain well-known methods of diminishing concentrations of nitrogen compounds, but they are ineffective in case of nitrogen-rich wastewater with a low content of biodegradable carbon. Partial nitritation followed by anaerobic ammonium oxidation (Anammox) process appear to be an excellent alternative for traditional nitrification and denitrification. This paper presents the feasibility of successful start-up of Anammox process in a laboratory-scale membrane bioreactor (MBR). It was shown that the combination of membrane technology and Anammox process allowed to create a new highly efficient and compact system for nitrogen removal. It was possible to achieve average nitrogen removal efficiency equal to 76.7 ± 8.3%. It was shown that the start-up period of 6 months was needed to obtain high nitrogen removal efficiency. The applied biochemical model of the Anammox process was based on the state-of-the-art Activated Sludge Model No.1 (ASM 1) which was modified for accounting activity of autotrophs (nitrite-oxidising bacteria and nitrateoxidising bacteria) and anammox bacteria. In order to increase the predictive power of the simulation selected parameters of the model were adjusted during model calibration. Readjustment of the model parameters based on the critically evaluated data of the reactor resulted in a satisfactory match between the model predictions and the actual observations.