Membrane capacitive deionization (MCDI) is a technique for water desalination by adsorbing ions in charged porous electrodes. In the present experimental and theoretical study, we analyze the performance, in terms of energy consumption, salt rejection and water recovery, of MCDI operated in intermittent flow mode. With this mode, the water recovery of MCDI is increased by reducing the water flow ratio during regeneration. Both experimental and theoretical results show that high values for water recovery and salt rejection can be achieved with a lab-scale MCDI system for feed water with a salinity of 40 mM. Importantly, we find that the energy requirement of MCDI is a factor of 2.0–2.5 higher than of RO. For RO, the energy requirements were calculated with a system-scale model developed by Qin et al. . Furthermore, we show that, based on our theoretical predictions, improved MCDI can reach high salt rejection and water recovery, without an additional energy penalty. In these conditions, the energy consumption of MCDI is lower than of RO. In the present work, we present new insights for a fair performance comparison of MCDI and RO.