A procedure of femtosecond pulse laser irradiation was incorporated into the synthesis of zinc oxide (ZnO) nanowires in aqueous solutions to investigate the photo-initiated heterogeneous nucleation induced by the irradiation and the associated nanowire growth. Elongated ZnO nanowires with smooth planes and end tips were successfully grown following the irradiation process and subsequent hydrothermal treatments in a catalyst-free environment, compared to aggregated flower-like nanostructures with porous and rough surfaces, grown from homogeneous nucleation without laser irradiation. Studies using femtosecond laser systems at 1 kHz and 250 kHz repetition rates show that the pulse energy is critical in the heterogeneous nucleation process for the growth of ZnO nanowires. A minimum threshold pulse energy, 200 microJ/pulse for the 1 kHz system and 2.4 microJ/pulse for 250 kHz, is observed beyond which well-defined and individually separated nanowires were grown. Thermal effect caused by the 250 kHz repetition rate provides a counter-balance to the low pulse energy required for the growth process. XRD analysis of the nanowires reveals a hexagonal structure while photoluminescence shows emission at about 385 nm. The overall results show that the pulse energy is critical for heterogeneous nucleation while the irradiation duration affects the density of nucleation, which together with the hydrothermal treatment temperature influence the growth rate and thus the morphology of the nanowires.