Electrophoretic deposition (EPD) has been demonstrated to be a convenient processing technique to fabricate composite ceramic coatings containing ordered arrays of carbon nanotubes. In this investigation, EPD was used to coat Ti6Al4V medical implants with hydroxyapatite (HA) layers reinforced with surface functionalized multi-walled carbon nanotubes (MWCNTs). The functionalization of MWCNTs by treating them with an acid mixture was successfully achieved in order to create functional groups on the MWCNT surfaces enabling them to be homogeneously dispersed in water. The surface treatment was also used to induce the adsorption of HA nanoparticles on MWCNT surfaces. Some critical issues, such as microcracking and peeling of HA layers after EPD, were effectively solved by the use of MWCNTs.