Background: Malaria is a major public health concern in the world and children are more vulnerable. Most studies conducted in Ethiopia by different researchers mostly focused on the adult population and high transmission areas. Hence, this study aimed to determine the prevalence and associated factors of malaria in children’s under the age of five years in low transmission areas. 

Method: A facility based cross-sectional study was conducted in Wogera district from September to October 2017. Health facilities were selected by stratified cluster sampling while systematic random sampling technique was held to reach under-five clients (with a minimum sample size of 585) attending public health facilities. Data were collected by a structured questionnaire containing sections of sociodemographic risk factors and knowledge and prevention practices of malaria. Binary logistic regression was used to identify the determinant factors of malaria.

Result: Of 585 children who provided blood samples, 51/585 (8.7 %) were confirmed for malaria parasites. The predominant Plasmodium species were P.falciparum 33 (65%) and P.vivax 18 (35%). Regularly sleeping under Insecticide Treated Nets (ITN) (AOR=0.08, 95% CI: 0.01-0.09) was significantly associated with decreased odds of malaria infection. However, an increased odds of malaria infection was observed among children living in households where there is stagnant water in the compound (AOR=6.7, 95% CI: 3.6-12.6) and children staying outside during night time (AOR=5.5, 95% CI: 2.7-11.1) compared to their counterparts.

Conclusion and recommendation: Prevalence of malaria in under -five children in Wogera was high. Regularly Sleeping under a bed net, staying outside during night time and presence of stagnant water around the household are the main factors associated with malaria that requires due attention in preventing malaria.  Therefore, low transmission areas should get better attention in terms of malaria prevention activities on modifiable factors such as ITN distribution, environmental management and changing attitude through health education.