Tuning the intrinsic structural and stoichiometric properties by different means is used for increasing the green energy production efficiency of complex oxide materials. Here, we report on the formation of self-assembled nanodomains and their effects on the photoelectrochemical (PEC) properties of LaFeO3 (LFO) epitaxial thin films as a function of layer’s thickness. The variation with the film’s thickness of the structural parameters such as in-plane and out-of-plane crystalline coherence length and the coexistence of different epitaxial orientation—<100>SrTiO3//<001> LFO, <100>SrTiO3//<110> LFO and [110] LFO//[010] STO, as well as the appearance of self-assembled nanodomains for film’s thicknesses higher than 14 nm, is presented. LFO thin films exhibit different epitaxial orientations depending on their thickness, and the appearance of self-assembled nanopyramids-like domains after a thickness threshold value has proven to have a detrimental effect on the PEC functional properties. Using Nb:SrTiO3 as conductive substrate and 0.5 M NaOH aqueous solution for PEC measurements, the dependence of the photocurrent density and the onset potential vs. RHE on the structural and stoichiometric features exhibited by the LFO photoelectrodes are unveiled by the X-ray diffraction, high-resolution transmission electron microscopy, ellipsometry, and Rutherford backscattering spectroscopy results. The potentiodynamic PEC analysis has revealed the highest photocurrent density Jphotocurrent values (up to 1.2 mA/cm2) with excellent stability over time, for the thinnest LFO/Nb:SrTiO3 sample, both cathodic and anodic behavior being noticed. Noticeably, the LFO thin film shows unbiased hydrogen evolution from water, as determined by gas chromatography in aqueous 0.5 M NaOH solution under constant illumination.