Thin films of Pr1-xCaxMnO3 (x=0.5,0.6) deposited on LaAlO3 and SrTiO3 substrates have been studied by Raman spectroscopy at low temperatures in order to investigate the effect of strains from the Ca doping or the substrate. A detailed assignment of the observed bands is suggested based on the present observations and published results on manganites. We assign the low frequency bands to modes involving only displacements of the A-site ions from their mass dependence by the Ca substitution for Pr (Pr/Ca–O modes). The Ag(2) mode, which is related to the tilting angle of the MnO6 octahedra, appears strongly coupled with the carriers and is very sensitive to the strain effects. Based on the Raman data obtained from the film cross sectional area, we extract the strain distribution across the film. Besides, we calculate in the pseudocubic approximation the phonon deformation potentials, the Grüneisen parameter, and the bulk modulus of the film, which are in good agreement with the ultrasonic measurements.