Background: Health inequalities may begin during childhood. The aim of this study was to investigate the main effect of poverty and its interactive effect with gender on children’s blood pressure. Methods: The study was performed in two elementary schools from a rural region near Podgorica, the capital of Montenegro. A questionnaire including questions on family monthly income, children’s physical activity and the consumption of junk food was self-administered by parents of 434 children (223 boys and 211 girls) aged 6–13 years. Children’s poverty level was assessed using the recommendations from the National Study on Poverty in Montenegro. Children’s body weight and height were measured and body mass index-for-gender-and-age percentile was calculated. An oscillometric monitor was used for measurement of children’s resting blood pressure in school. Results: A two-factorial analysis of variance with body mass index percentile, physical activity and junk food as covariates showed an interaction of gender and poverty on children’s blood pressure, pointing to synergy between poverty and female gender, with statistical significance for raised diastolic pressure (F = 5.462; P = 0.021). Neither physical activity nor the consumption of junk food explained the interactive effect of poverty and gender on blood pressure. Conclusion: We show that poverty is linked to elevated blood pressure for girls but not boys, and this effect is statistically significant for diastolic pressure. The results are discussed in the light of gender differences in stress and coping that are endemic to poverty.