Abstract This study is developed to evaluate the possibility of R1234yf to be a drop-in replacement for a pre-designed system with R134a, including the characterization of control system in a vapor compression system. The control algorithms are required for regulating the refrigerant flow rate into the evaporator and their control parameters depend intrinsically on refrigerant fluid. This paper presents a comparison of the effects of R134a and R1234yf refrigerants on the transient response of an evaporator operating with water as secondary fluid (counter-flow). The dynamic heat exchanger distributed model combines principles of thermodynamics, heat and mass transfer with empirical correlations, which are proposed in the literature, in order to compute the void fraction, pressure drop and heat transfer in two-phase flow. Experimental tests are carried out on a fixed refrigeration system for cooling capacity less than 3 kW, with constant condensation conditions, variable evaporating temperature and compressor speed to validate the model. The results demonstrated that a good agreement between simulation results and experimental data was achieved. The evaporation temperature data were within ± 1 °C error band. Furthermore, comparative simulations between the refrigerants R-134a and R-1234yf exhibited a similar dynamic behavior during a step at the inlet mass flow rate, and the gain and time constant for superheat control were not considerably modified. Therefore, the refrigerant changing does not demand many changes in the expansion device control strategy.