TiO2 thin films are known to promote photodegradation of dyes and pollutants in water solution via heterogeneous photocatalysis. This ability is guided by the photoexcitation through photons having energies above the band gap. To improve photocatalytic activity, nanostructures with high surface area can be applied, which can ease molecular adsorption/desorption mechanisms, enhance electronic transfer properties and lower excitation energy. For this purpose, square cross-section TiO2 vertically aligned nanorod (TNR) array configuration has been chosen as a semiconductor substrate. On top of it, a thin layer of sub-stoichiometric TiO2−x has been deposited, aiming at inducing a vacancy doped homojunction between two different oxygen rich/deficient TiO2 layers, possibly leading to lower band gap and enhanced photochemical activity. In principle, promotion of electron and holes separation and suppression of charge recombination could occur. Vertically aligned TNRs have been deposited through a hydrothermal growth in acidic conditions on a pre-seeded glass conducting substrate, optimizing the seeding process through spin coating. Sub-stoichiometric TiO2−x layer (50 nm nominal thickness) has been deposited on top of TNRs via radiofrequency magnetron sputtering at three different stoichiometries, tuning the oxygen partial pressure in sputtering argon atmosphere at 10 %, 15 % and 20 %, respectively. Photocatalytic activity has been investigated in the photodegradation of an aqueous solution of methylene blue, both under UV and simulated solar light irradiation at room temperature and atmospheric pressure, resulting in the degradation of methylene blue target molecule up to 99 % under UV and 85 % under simulated solar irradiation after 6 h. These promising achievements unlock new environmental applications for enhanced dye degradation industrial processes.