Malaria and undernutrition pose challenges for children in conflict-affected areas. Understanding the prevalence and risk factors for these issues in war-torn communities is important to effectively design aid efforts and select interventions. This study aimed to determine the prevalence and correlates of malaria and undernutrition among febrile children in northeast Ethiopia to help address these problems. A cross-sectional study was conducted from November 2022 to January 2023. Four hundred twenty-two children were enrolled using a systematic random sampling technique. Data on associated factor variables were collected via questionnaire. Capillary blood samples were collected from each child to prepare thick and thin blood films, which were stained with Giemsa and examined microscopically. Height and weight measurements were also taken using a meter and a standard calibrated balance. The data were analyzed in SPSS 26.0 using bivariable and multivariable logistic regression to determine associations between correlates, malaria infection, and undernutrition. Statistical significance was set at p < 0.05. The overall malaria prevalence among screened children at temporary sites in the conflict-affected areas of Northeast Ethiopia was 65.9% (278/422). Plasmodium falciparum, P. vivax, and mixed infections accounted for 74.1%, 19.8%, and 6.1% of the cases, respectively. The presence of stagnant water (P<0.01), improper utilization of ITN, inadequate number of ITNs per family size (P<0.01), and absence of environmental management (P<0.01) were independent predictors of malaria. On the other hand, the overall undernutrition prevalence was 54.7% (231/422), including 26.5% underweight, 16.8% stunted, and 11.4% wasted. Dietary diversity score (P<0.01), meal frequency (P<0.01), and confirmed malaria infection (P<0.01) were significantly associated with underlnutrition. Both malaria and undernutrition burdens were high among the children in this study. The findings suggest combined prevention measures for malaria and undernutrition should be strengthened in this region.