A volume-averaged model is used to study the self-pulsing operation of a micro hollow cathode discharge in helium. An equivalent circuit with a nonlinear resistance is employed to model the discharge in this regime. The effects of the applied voltage and the gas pressure on the self-pulsing frequency, particle densities, and electron temperature are carefully studied. The simulation results are also compared with those of the argon micro hollow cathode discharge. The results show that the time-averaged densities in the self pulsing regime are close to the steady-state densities. Both the applied voltage and the background gas pressure have remarkable effects on the self pulsing frequency and consequently on the average densities. However, the pressure effects are much stronger than those of the applied voltage. The results also indicate that there is an optimum pressure, in which PD (D is the diameter of the hole) reaches its upper limit, and the electron density is maximized. By further increase in the pressure, the electron density declines. However, the densities of the excited particles are independent of PD and always increase with the increase in pressure. It is also found that the electron density in the helium discharge is less than that of the argon. But, the reverse is true for the electron temperature. The higher electron temperature in the helium discharge is a key factor in increasing the efficiency of production of the reactive species.