Background: Malnutrition affects many children in Africa predisposing them to infection especially bacterial. Although malnutrition is highly prevalent among Nigerian children little is known about bacterial infection which is believed to adversely affect their outcome. Materials and Methods: This was a cross-sectional study. Ninety febrile children with severe Protein Energy Malnutrition aged 6–59-month based on modified wellcome classification were enrolled as individuals and; 90 febrile well-nourished children age- and sex-matched as controls. It was conducted at the emergency pediatrics unit of Aminu Kano Teaching Hospital from May to October 2013. Bacteremia was diagnosed using automated BACTEC method and Kirby-Bauer disk diffusion technique was used for antibiotic sensitivity. Results: Bacteremia occurred in 45.6% of the individuals which was significantly higher than 23.3% in the control group (odds ratio = 2.56, confidence interval = 1.45–5.22). Staphylococcus aureus(41.5%), Escherichia coli (17.1%), and Salmonella typhi (12.2%) were the most frequent isolates in the individuals. 87.8% of the isolates in the individuals were sensitive to ciprofloxacin, 85% to ceftriaxone, 51% to gentamicin, but very low sensitivity to amoxicillin (22%) and cotrimoxazole (12.1%). Conclusion: Bacteremia is highly prevalent among the malnourished children and the commonest isolate was S. aureus. The isolates were most sensitive to ciprofloxacin and ceftriaxone.