Background Measuring height for age is one of the essential indicators for evaluating children’s growth. The study analyzes the association between maternal education and stunting among children under two years in Indonesia. Methods The study employed secondary data from the 2017 Indonesia Nutritional Status Monitoring Survey. The unit of analysis was children under two years, and the study obtained weighted samples of 70,293 children. Besides maternal education, other independent variables analyzed in this study were residence, maternal age, maternal marital status, maternal employment, children’s age, and gender. In the final stage, the study occupied a multivariate test by binary logistic regression test. Results The results show the proportion of stunted children under two years in Indonesia nationally is 20.1%. Mothers in primary school and under education categories are 1.587 times more likely than mothers with a college education to have stunted children under two years (95% CI 1.576–1.598). Meanwhile, mothers with a junior high school education have a chance of 1.430 times more than mothers with a college education to have stunted children under two years (95% CI 1.420–1.440). Moreover, mothers with education in the senior high school category have 1.230 times more chances than mothers with a college education to have stunted children under two years (95% CI 1.222–1.238). Conclusion The study concluded that the maternal education level was associated with stunting children under two years in Indonesia. The lower the mother’s level of education, the higher the chances of a mother having stunted children under two years.