BackgroundDouble burden of childhood malnutrition is a condition where undernutrition (stunting) along with overweight and obesity coexist within individuals, households, and populations. It reflects a new layer of malnutrition and an understudied phenomenon in many low-income settings. To date, the prevalence and factors that are associated with concurrent stunting and overweight or obesity (overweight/obesity) (CSO) in the same children have not been well researched in Ethiopia. Hence, this study aimed to assess the prevalence, trends, and factors associated with the coexistence of stunting and overweight or obesity among children aged 0–59 months in Ethiopia.MethodsPooled data from 2005, 2011 and 2016 Ethiopian Demographic and Health Survey (EDHS) were used. A total of 23,756 (weighted sample) children aged 0–59 months were included in the study. Height-for-age z-scores (HAZ) less than − 2 SD and weight-for-height z-scores (WHZ) above 2 SD were calculated, and children were classified as stunted and overweight/obese, respectively. A child who is simultaneously stunted and overweight/obese was considered as having HAZ below − 2 SD and WHZ above 2 SD computed into a variable named CSO, and reported as a binary outcome (yes or no). Multilevel logistic regression analysis that adjusts for sampling weights and clustering was used to identify factors associated with CSO.ResultsThe prevalence of stunting, overweight or obesity, and CSO among under-five children was 43.12% [95% CI: (42.50, 43.75%)], 2.62% [95% CI: (2.42, 2.83%)], and 1.33% [95% CI: (1.18, 1.48%)], respectively. The percentage of CSO children was reported to have declined from 2.36% [95% CI: (1.94–2.85)] in 2005 to 0.87% [95%CI: (0.07–1.07)] in 2011, and the same appeared to have increased slightly to 1.34% [95%CI: (1.13–1.59)] in 2016. Children who were currently breastfeeding [AOR: 1.64, 95%CI: (1.01–2.72)], born to an overweight mother [AOR: 2.65, 95%CI: (1.19–5.88)], and lived in families with 1–4 household members [AOR: 1.52, 95%CI: (1.02–2.26)] were significantly associated with CSO. At the community level the odds of having CSO were higher among children included from EDHS-2005 [AOR: 4.38, 95%CI: (2.42–7.95)].ConclusionThe study revealed that less than 2% of children had CSO in Ethiopia. CSO was linked to factors at both the individual (i.e. breastfeeding status, maternal overweight, and household size) and community-levels. Overall, the study findings indicated the necessity of focused interventions to simultaneously address double burden of childhood malnutrition in Ethiopia. To further combat the double burden of malnutrition, early identification of at-risk children, including those born to overweight women and children living with multiple household members, is indispensable.