Objectives This study aimed to determine the relationship between stunting in children 6 to 36 months old and maternal employment status in Peru. Methods A secondary data analysis was conducted using information from the Demographic and Health Survey (DHS) in Peru. We used a representative sample of 4637 mother-child binomials to determine the association between stunting in children 6 to 36 months of age and the employment status of their mothers. Results The prevalence of stunting among children was 15.9% (95% CI: 13.9–16.7). The prevalence of working mothers was 63.7%. No association was found between maternal employment status and the presence of stunting in children [prevalence ratio (PR) = 1.04; 95% confidence interval (95% CI): 0.9 to 1.2; p = 0.627). However, on multivariate analysis we found that the prevalence of stunting was significantly higher among children of mothers performing unpaid work (12.4%) (PR = 1.38; 95% CI: 1.2–1.6; p < 0.001) compared with those of paid working mothers. Conclusion No significant association was found between maternal employment status and the presence of stunting in children 6 to 36 months of age. However, children of mothers doing unpaid work are at higher risk of stunting. These findings support the implementation of educational programs and labour policies to reduce the prevalence of stunting among children.