Cobalt oxide nanoparticles were sensitized on hydrothermally grown TiO2 nanorods on FTO (fluorine-doped tin oxide) by electrochemical deposition, followed by rapid thermal annealing under air and N2. We investigated the formation of the nanostructure with different electrodeposition times, electrolyte concentrations, and annealing temperatures for improved photoelectrochemical (PEC) properties. A structural investigation showed the formation of a mixture of CoO/Co3O4 oxides dependant on annealing temperature and atmosphere. The oxide formation equilibrium shifted from Co3O4 to a mixture of CoO/Co3O4 and finally to monoxide when temperature is lowered from 700°C to 350°C. Improved PEC properties were shown by the mixture of oxides compared to a system with CoO and Co3O4 alone on TiO2. Electrodeposition time was found to have a linear relationship with the nanoparticle size of cobalt oxide formed on TiO2. Here we propose a cost effective and simple method to fabricate a hetero-junction system with improved PEC properties.