Background: Malaria is a major public health problem affecting humans, particularly in the tropics and subtropics. Children under 5 years old are the group most vulnerable to malaria infection because of less developed immune system. Countries have set targets that led to control and eliminate malaria with interventions of the at-risk groups, however malaria infection remained a major public health challenge in endemic areas. Objective: This study aimed at determining the magnitude of malaria and associated factors among febrile children under 5 years old in Arba Minch "Zuria" district. Methods: The study was conducted from April to May 2017. Blood samples were collected from 271 systematically selected febrile children under 5 years old. Thin and thick blood smears were prepared, stained with 10% Giemsa and examined under light microscope. Data of sociodemographic data, determinant factors, and knowledge and prevention practices of malaria were collected using a pretested structured questionnaire. Data were analyzed using binomial and multinomial regression model in SPSS ® Statistics program, version 25. Results: Among those febrile children, 22.1% (60/271) were positive for malaria; 50.0%, 48.33% and 1.66% of them were positive for Plasmodium falciparum, Plasmodium vivax and mixed infections of both parasites, respectively. Malaria infection was associated with nearby presence of stagnant water to resident areas (AOR=8.19; 95%CI: 3.62-18.5, P<0.0001). Children who slept under insecticide-treated mosquito nets (ITNs) were more likely to be protected from malaria infection than those did not sleep under an ITNs (AOR=9.65; 95%CI: 4.623-20.15, P<0.0001). Conclusion: Malaria infection is highly prevalent in children aged between 37 and 59 months old, in Arba Minch "Zuria" district. The proximity of residence to stagnant water and the use of ITNs are the most dominant risk factor for malaria infection. Improved access to all malaria interventions is needed to interrupt the transmission at the community level with a special focus on the risk groups.