Abstract Background Data on the effect of maternal daily work hours on child nutritional status is scarce in Ghana. Such data may be important in defining maternal employment policies for improved child nutrition. This study therefore sought to determine the effect of maternal daily work hours on the nutritional status of farmer and public service mothers in the northern region of Ghana. Methods An analytical cross-sectional survey was conducted among 320 mothers with children 6–59 months. Maternal daily work hours and dietary intake of children were assessed with a structured questionnaire. Anthropometric measurements of children were also taken to classify child nutritional status. The association between maternal daily work hours and child nutritional status was determined using both bivariate analysis and multivariate regression modelling. Results Majority of the children (45.1%) were aged between their second and third birthdays. The prevalence of stunting, wasting, and underweight were 17.8, 8.1, and 10.3% respectively. Only stunting (p = 0.031) associated significantly with maternal employment and was higher among children of farmers (22.1%) compared to public servants (12.8%). Even though maternal age (p = 0.035), minimum dietary diversity (p = 0.040), non-consumption of legumes (p = 0.031) and other vegetables (p = 0.006) associated with stunting at bivariate level, multivariate logistic regression analysis revealed that only maternal daily work hours had significant effect on stunting. Compared to mothers who worked above 6 h a day, those who worked only a maximum of 4 h were 5.4 times more likely to have stunted children [AOR = 5.375; 95% CI (1.751–16.502); p = 0.003]. Conclusion Present study results show that maternal daily work hours could be an important determinant of child stunting in northern region of Ghana.