In this paper, we present a comparative numerical analysis to determine the refractive index of photonic crystal fibers (PCFs) by using FDFD method and used the results to evaluate the confinement losses of PCFs by considering the effects of air-hole rings in the cladding. It is shown that by increasing the wavelength, the imaginary part of refraction index rises, resulting in increase of confinement losses nearly by order of 10. In lower wavelengths over the range of 0.2 to 1 μm, these losses were shown to be negligible. The obtained results show that as the number of air-hole ring in the cladding increases, the confinement losses over wavelengths would reduce. To show the effect of air-hole rings on confinement losses in PCFs, the FDFD method yielded accurate results that agree well with results of FEM method and source–model technique reported by others.