Humans are exposed to electromagnetic fields (EMF) from various sources throughout life. Because humans are easily impacted by environmental factors during early development, it is believed that EMF can cause structural and functional changes on the developing brain that may lead to behavioural changes. This paper investigates the impact of EMF exposure and zinc supplementation during the prenatal and postnatal periods on behavioural changes and synaptic proteins in a gender-dependent manner. Pups from four groups of pregnant rats were used: Sham, EMF (5 days/wk, 4 h/day EMF-exposure applied), Sham+Zinc (5 days/wk, 5 mg/kg/day zinc applied) and EMF+Zinc (5 days/wk, 4 h/day EMF-exposure and 5 mg/kg/day zinc applied). EMF exposure and zinc supplementation were initiated from the first day of pregnancy to the 42nd postnatal day. Zinc levels in blood, NLGN3 and SHANK3 levels in hippocampus and amygdala, and synaptic structures in amygdala were examined. Behavioural tests showed that EMF exposure had no effect on social behaviour, but adversely affected activity and exploratory behaviour, and led to increased anxiety formation. Zinc supplementation had a partially positive effect on female, but not male offspring. SHANK3 and NLGN3 proteins were significantly lower in EMF groups, however, no positive effect of zinc supplementation was found. In conclusion, EMF exposure may alter the levels of synaptic proteins in the developing brain, leading to behavioural changes in a gender-dependent manner. Evaluation of zinc supplementation at different doses could be beneficial to prevent or reduce the behavioural and structural effects of EMF.