BackgroundMotivating proper nutrition during childhood is the basis for optimal health, learning, productivity, and social wellbeing throughout life. Stunting is among the major public health problems. According to the Ethiopian mini demographic and health survey, the prevalence of stunting among under five children was 37%. In addition, stunting has a trans-generational effect on a mother’s nutritional status. However, evidence on the causal contribution of maternal employment to stunting among under five children is not well understood in Ethiopia. This study aimed to compare the stunting status and associated factors among under five children of employed and unemployed mothers in the Gurage Zone, Southern Ethiopia, in 2021. A community-based comparative cross-sectional study was conducted among 671 (330 employed and 341 unemployed) randomly selected mother–child pairs in the Gurage Zone, Southern Ethiopia. A pretested semi-structured tool and validated anthropometric measurements were used to collect the data. The data were entered into Epi Data version 3.1 and exported to Statistical Package for Social Science (SPSS) version 23.0 for analysis. Frequency, percent, mean, median, and SD were computed and presented by using tables and figures. A bivariable and multivariable binary logistic regression analysis was conducted to assess the association between factors and outcome variables.ResultsIn this study, a total of 671 mother–child pairs (330 (94.60%) employed and 341 (97.70%) unemployed) participated, with a total response rate of 96%. Among the total participants, about 70 (21.2%) [95% CI: (17.0, 25.5)] and 98 (28.8%) [95% CI: (23.0, 33.4)] of children of employed and unemployed mothers, respectively, were stunted. Mothers’ level of education, primary and secondary [AOR = 1.79, 95% CI: (0.8, 3.7), age between 25 and 29 years [AOR = 0.08, 95% CI: (0.006, 0.904)], monthly family income > 5,000 birr [AOR = 0.42, 95% CI: (0.00, 0.64)], and children aged between 6 and 23 months [AOR = 2.9; 95% CI: (1.48, 5.80)] were predictors of stunting among the children of employed mothers. Compared to the mothers who did not receive nutritional education [AOR = 2.5; 95% CI: (1.10, 5.60)], monthly family income of 2,000 ETB [AOR = 2.64; 95% CI: (1.34, 5.19)], sex of child (girl) [AOR = 2.3; 95% CI: (1.30, 3.80), and mothers educational status of read-and-write only [AOR = 2.9, 95% CI: (1.40, 5.80)] were predictors of stunting among the children of unemployed mothers. The nutrition intervention should focus on encouraging women’s education as it increases the probability of being employed, improving the income of families by using different income-generating strategies, and strengthening the existing essential nutrition counseling strategy. Likewise, further research work on the difference between employed and unemployed mothers on stunting status is also recommended to researchers.