The effect of the pulsed electron beam (PEB) treatment on the structure and morphology of the hydroxyapatite (HA) coating deposited on the surfaces of titanium substrates by radio frequency magnetron sputtering was elucidated. The structure, composition and morphology of the samples were characterized by scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD). The results collected from SEM experiments demonstrated that the HA film was smooth and featureless. The samples were irradiated by PEB using an electron beam energy density of 0.1Jcm−2, electron beam pulse duration of 50μs, pulse repetition frequency of 5Hz, and number of pulses N=50 and N=150. After PEB treatment with N=50, the coating exhibited a much finer uniform surface morphology, playing a crucial role in the enhancement of the mechanical properties of the HA-coated titanium substrate. The surface of the HA film treated with N=150 was still smooth and featureless. The XRD data demonstrated that PEB treatment of HA films produced only a slight decrease in the HA phase content. The combination of these two techniques opens the possibility of preparing high quality HA layers.