Micro-ORC systems are usually equipped with positive displacement machines such as expanders and pumps. The pumping system has to guarantee the mass flow rate and allows a pressure rise from the condensation to the evaporation pressure values. In addition, the pumping system supplies the organic fluid, characterized by pressure and temperature very close to the saturation. In this work, a CFD approach is developed to analyze from a novel point of view the behavior of the pumping system of a regenerative lab-scale micro-ORC system. In fact, starting from the liquid receiver, the entire flow path, up to the inlet section of the evaporator, has been numerically simulated (including the Coriolis flow meter installed between the receiver and the gear pump). A fluid dynamic analysis has been carried out by means of a transient simulation with a mesh morphing strategy in order to analyze the transient phenomena and the effects of pump operation. The analysis has shown how the accuracy of the mass flow rate measurement could be affected by the pump operation being installed in the same circuit branch. In addition, the results have shown how the cavitation phenomenon affects the pump and the ORC system operation compared to control system actions.