Methods The community-based cross sectional study was conducted in the Arba Minch Health and Demographic Surveillance Site, Southern Ethiopia. The simple random sampling method was used to recruit 656 mother-child pairs. Height for age Z score was computed using WHO Anthro version 3.2.2 software. Multivariable logistic regression model was fitted, and adjusted odds ratio (AOR) at p value <0.05 was used to determine statistically significant association between predictors and outcome variable. Result The prevalence of stunting among children of 6–59 months in the study area was 47.9% (95% CI; 44.0–51.7). The likelihood of stunting was significantly higher among children who live in households with medium (AOR 2.20, 95% CI: 1.43–3.37) and poor (AOR 2.87, 95% CI: 1.72–4.81) wealth status. In addition, children who were not exclusively breast fed (AOR 1.55, 95% CI: 1.07–2.24), whose mothers had not participated in decision of major household purchases (AOR 2.27, 95% CI: 1.21–4.26), and whose mothers lacked decision on freedom of mobility (AOR 1.96, 95% CI: 1.05–3.66) were significantly stunted compared with counterparts. Conclusion Stunting is a severe public health problem in the area. Therefore, efforts should be taken to enhance maternal empowerment, household wealth, and infant and young child feeding practice for reducing stunting among children.