This paper intends a Euler-Lagrange passivity-based controller (EL-PBC) for the three-level (TL) Ćuk PFC converter for EVs battery charging application. The TL Ćuk converter has features of reduced filter size and voltage stress of switches. First, the Euler-Lagrange formulation is used to develop the mathematical modelling. Then, the EL-PBC methodology is implemented by injecting a virtual resistor in series with the input inductor. Further, the stability analysis is also carried out. To improve the performances against input perturbations and reduce the steady state error, a PI controller is integrated with the aforesaid controller and its performances are investigated. Furthermore, the power quality of the charger is assessed and it satisfies IEC 61000-3-2 Class C standard. This controller is also compared with the benchmark PI controller. A prototype model of same specifications is tested in hardware in loop. Computer simulations and test results are presented to validate the theoretical aspects.