Zinc oxide nanoparticles (ZnO NPs) are ones of the most commonly manufactured nanomaterials worldwide. They can be used as a zinc fertilizer in agriculture to enhance yielding and to control the occurrence of diseases thanks to its broad antifungal and antibacterial action. The aim of this study was to investigate and compare the effects of ZnO submicron particles (ZnO SMPs) and ZnO NPs on the process of in vitro seed germination and seedling growth in onion (Allium cepa L. ‘Sochaczewska’), and to indicate the potential use of these compounds in onion production. In the experiment, disinfected seeds were inoculated on the modified Murashige and Skoog (MS) medium and poured with ZnO SMP or ZnO NP water suspension, at the concentrations of 50, 100, 200, 400, 800, 1600, and 3200 mg∙L−1. During three successive weeks, the germinating seeds were counted. Germination started most often on the second or third day of in vitro culture. The highest share of germination was recorded for seeds treated with 800 mg∙L−1 ZnO SMPs and ZnO NPs (52% and 56%, respectively). After the application of ZnO SMPs and ZnO NPs at the highest tested concentration (3200 mg∙L−1), the share of germinating seeds was only 19% and 11%, respectively. Interestingly, seedlings obtained from control seeds and seeds treated with ZnO SMPs and ZnO NPs did not differ statistically in terms of length, fresh weight, and dry weight of leaves, and roots. Both ZnO SMPs and ZnO NPs, in the concentration range from 50 to 1600 mg∙L−1, can be used to stimulate the germination process of onion seeds, without negative effects on the further growth and development of seedlings. There were no differences found between the action of ZnO NPs and ZnO SMPs, which suggested that the most important factor influencing seed germination was in fact the concentration of zinc ions, not the particle size.