Background: Malaria remains a significant public health challenge in Somalia, with varying prevalence influenced by environmental, demographic, and regional factors. Mogadishu, as a major urban center, presents unique malaria dynamics requiring localized data for effective control. This study analyzes malaria prevalence and testing patterns at Kalkaal Hospital, using gold standard diagnostic test microscopy and malaria rapid diagnostic tests, from January to October 2024. Methods: A retrospective analysis was conducted on malaria diagnostic records, including 11,497 tests performed at Kalkaal Hospital's hematology department. Data collected included test results, patient demographics, service settings (inpatient/outpatient), and department-specific testing patterns. Standard microscopy and malaria rapid diagnostic were employed for diagnosis. Statistical analysis assessed positivity rates and identified testing trends. Results: Out of 11,497 tests, 10 cases (0.087%) were confirmed positive, while 11,487 (99.913%) were negative. The outpatient department accounted for 80% of positive cases, with obstetrics and gynecology contributing the highest proportion (30%), followed by internal medicine/cardiology and pediatric services (20% each). The highest testing volumes were recorded in emergency (3,247 tests) and pediatric services (2,683 tests). Monthly data showed a peak in positive cases during January (6 cases) and April (2 cases), suggesting seasonal influences on malaria transmission. Conclusions: This study found an exceptionally low malaria prevalence in Mogadishu, reflecting low malaria infection rates in Mogadishu Somalia. This is in coherence with recent studies that suggest Mogadishu, Somalia, may be transitioning towards a non-malaria zone. However, the low positivity rate suggests potential overuse of malaria testing for febrile illnesses in this urban setting.