Background: Malaria is associated with an increase in viral load and fall in CD4-cell count. This study was carried out to estimate the prevalence of malaria among HIV patients in hospitals. Method: This was a descriptive cross-sectional study that reviewed HIV patients’ folders in hospitals in Ghana. Ethical approvals were obtained from three recognized Ethical Review Committees. Result: The total 933 patients were made of 272 (29.2%) males and 661 (70.8%) females. A prevalence of 4.4% (95% CI: 2.2, 6.6) confirmed cases of malaria was recorded in the study. Fever, was not significantly associated with confirmed malaria (OR=3.11, 95% CI: [0.63, 15.37], P=0.142). Conclusions: A low prevalence of confirmed malaria, 4.4% (95% CI: 2.2, 6.6), was recorded among HIV patients from Ghana. The prevalence could also be attributed to the high cases of malaria diagnosed presumptively (37.0%), (OR=4.11, 95% CI: [2.83, 5.96], P<0.001). Evidence based diagnoses and treatment of malaria should be improved. Demographic characteristics, CD4 count levels and ART status of patients were not significantly associated with malaria. This may be due to the poor records keeping at all sites.