A method of fabricating oriented single-crystalline SrRuO3 nanowire arrays using a bottom-up approach relying on diffusion-controlled self-organization is demonstrated. DyScO3 substrates exhibiting an ordered striped phase of DyO and ScO2 chemical termination are used as a template for pulsed laser deposition growth of SrRuO3. Here SrRuO3 preferentially nucleates on one type of termination. The resulting nanowires are single crystalline, conducting and isolated from each other, typically 100 nm wide and 5–10 nm high. This preferential growth is studied using a kinetic Monte Carlo model, which provides a guide to optimize growth conditions and tune the dimensions of the nanowires.