Electromagnetic field (EMF) and its effect on crop plant growth and their quality parameters is increasingly gaining the interest of researchers in agronomic science. However, the exact mechanism of EMF action in plant cells is still unclear. Among the completely unexplored parameters is the relationship between the EMF effects and the seed size. Thus, the EMF effect was analyzed in winter wheat seeds categorized into two size groups, small and big. The study focused on the germination kinetics, early growth parameters, and phytohormone concentrations (indole-3-acetic acid, IAA and abscisic acid, ABA) in seeds, roots, and coleoptiles after exposure to EMFs (50 Hz, 7 mT) and their controls. EMF exposure resulted in faster germination and the more rapid early growth of organs, especially in big seeds in dark conditions. The faster germination and seedling growth of small seeds in control conditions, and of big seeds after EMF exposure, corresponds largely to the decline in IAA and ABA levels. This study confirms that presowing treatment with an EMF is a promising tool for sustainable seed crop improvement, but detailed studies on the EMF mechanism of action, including phytohormones, are necessary to better control future crop yield, especially considering the factor of seed size.