Background: Malaria and bacterial bloodstream infections (BSIs) continue to be major causes of febrile illness and death in Nigeria. These infections often occur together, creating significant diagnostic and treatment problems, though little is known about the prevalence and risk factors for these infections in the north-eastern part of Nigeria. This study aimed to determine the prevalence, distribution, and predictors of malaria-BSI co-infections among febrile patients attending Federal Medical Centre (FMC), Jalingo, Taraba State. Methods: A retrospective cross-sectional study was conducted using secondary data from hospital records of 310 febrile patients who attended FMC Jalingo between 2023 and 2025. Malaria test results, blood culture results, demographic data, and clinical data were collected and analyzed with descriptive statistics, chi-square tests, and binary logistic regression. Results: The overall prevalence of malaria parasitemia was 61.9% (192/310; 95% CI: 56.4%–67.2%), while bacterial BSIs were detected in 32.6% (101/310; 95% CI: 27.6%–38.0%) of patients. The proportion of malaria-BSI co-infection was 23.5% (73/310; 95% CI: 19.2%–28.6%). Co-infections among children had the highest burden among all age groups (31.3%), followed by those aged 5–14 years (24.4%). Rural residence was an independent predictor of co-infection (adjusted OR = 2.133; 95% CI: 1.226–3.713; p = 0.007). HIV/AIDS (p = 0.014) and diabetes mellitus (p = 0.031) were significantly associated with co-infection. Conclusion: The prevalence of malaria-bacterial BSI co-infection in this group is about 25%, and young children, rural residents, and immunocompromised individuals are the highest-risk groups. The results emphasize the importance of integrated approaches to diagnosis, strengthening of laboratory capacity, and targeting interventions to high-risk groups in malaria-endemic areas in Nigeria.