Background: The prevalence of under nutrition is very high in developing countries such as Ethiopia. However there is limited information on the magnitude of undernutrition in conflict affected and not-conflict affected districts. This research will be essential for designing nutrition intervention in conflict affected districts . Objective: To compare the magnitude of undernutrition and its associated factors among children age 6-59 months in armed conflict and not- armed conflict affected districts in south Gondar zone, North West Ethiopia, 2022 Methods: A community based comparative cross sectional study design was conducted and 415 participants for armed conflict and 415 participants for not-armed conflict affected area were selected by systematically random sampling from October 20 to November 30, 2022. Data were collected using face to face interviewer administered questionnaire and entered in to Epi data and exported to SPSS version 25 for analysis. Pretested and structured questionnaire was used to collect data. The WHO Anthro was used to convert raw anthropometric data into Z-scores. Binary logistic regression and multivariable logistic regression analyses were done. A p-value less than 0.05 of were considered to declare a result as statistically significant. Results: The prevalence of under-nutrition among children aged 6-59 months in armed conflict affected district was higher than not-armed conflict districts 70.6% (95% of CI ; 65.5-74.5) and 56.3% (95% of CI: 51.7-61.1) respectively. In not-armed conflict affected districts children 13-24 months of age(AOR=2.17(1.46-3.25), being male (AOR=1.78, CI, 1.322-2.40), having resparatory tract infection (AOR= 1.48, 95% CI,1.02-2.12),complementary feeding (AOR=0.68, CI, 0.47-0.99) and household food security (AOR= 0.69, 95% CI, 0.51-0.93) were the factors associated with undernutrition in armed conflict affected districts, Whereas being male (AOR= 1.55, CI, 1.05-2.33) and low dietary diversity (AOR= 1.80, CI, 1.14-2.864) were the main predictors of undernutrition in not-armed conflict affected districts. Conclusion: Undernutrition is an important public health problem among underfive children in the study area. The prevalence of undernutrition was higher among armed conflict affected than not-armed conflict affected districts .Therefore, strengthening nutrition intervention considering timely initation of complementary feeding, improve house holds food security status and dietary diversity. Keywords: under-nutrition, 6-59 months children, armed conflict and not- armed conflict affected districts,South Gondar , Ethiopia