The purpose of this study was to investigate the electrochemical characteristics of silicon-substituted hydroxyapatite coatings on the nanotube-formed Ti–35Nb–10Zr alloy. The silicon-substituted hydroxyapatite (Si–HA) coatings on the nanotube structure were deposited by electron beam-physical vapor deposition and anodization methods, and biodegradation properties were analyzed by potentiodynamic polarization and electrochemical impedance spectroscopy measurement. The surface characteristics were analyzed by field-emission scanning electron microscopy, energy-dispersive X-ray spectroscopy and X-ray diffraction (XRD). The Si–HA layers were deposited with rough features having highly ordered nanotube structures on the titanium alloy substrate. The thickness of the Si–HA coating was less than that of the HA coating. The XRD results confirmed that the Si–HA coating on the nanotube structure consisted of TiO2 anatase, TiO2 rutile, hydroxyapatite, and calcium phosphate silicate. The Si–HA coating surface exhibited lower Icorr than the HA coating, and the polarization resistance was increased by substitution of silicon in hydroxyapatite.