Background: Malaria continues to be a significant public health concern, particularly in sub-Saharan Africa and other regions with high endemicity. Despite ongoing efforts to control the disease, the malaria parasite remains a global health issue, presenting persistent challenges for individuals and healthcare systems in affected areas. Methods: This study investigated the distribution, prevalence, and molecular characteristics of Plasmodium falciparum among febrile patients in various healthcare facilities within the Federal Capital Territory (FCT), Nigeria. A combination of retrospective and cross-sectional designs was employed to analyse 428 blood samples collected from febrile patients across selected government hospitals. Malaria parasitaemia was detected through Giemsa-stained thick and thin blood smears, with parasite density calculated per 200 leukocytes. RDT-prevalence wax determined using a rapid lateral flow. Result: A total of 428 individuals participated in the study, comprising 49.0% males (n=210) and 50.9% females (n=218), with no statistically significant difference in gender distribution (p>0.05). The age distribution showed that participants aged ≥41 years represented the largest group at 34.3% (n=147), while those aged <10 years accounted for 14.0% (n=60), 11–20 years for 16.1% (n=69), 21–30 years for 19.2% (n=82), and 31–40 years for 16.4% (n=70). Microscopic examination revealed a malaria infection rate of 32% (n=137) among participants, with the highest prevalence in those aged <10 years (33.6%, n=46) and the lowest in the 31–40 age group (8.8%, n=12). Gender-based analysis indicated a higher prevalence in males (52.6%) compared to females (47.4%). Facility-based prevalence was significantly higher in Wuse (30.0%, n=41) compared to other locations, with Zuba showing the lowest prevalence (8.0%, n=11). Rapid Diagnostic Test (RDT) results indicated a prevalence of 20.1%, with Wuse again exhibiting the highest rate at 38.6% (n=27/70). Age-related RDT prevalence showed the highest seroprevalence in the <10 years age group (65.0%, n=39/60), followed by 11–20 years (24.6%, n=17/69), 21–30 years (12.3%, n=10/81), and ≥41 years (8.8%, n=13/147). Conclusion: The findings reveal a slight predominance of females over males, indicating that women may be more inclined to seek medical attention for malaria-related symptoms. The malaria prevalence rate of 32.0% underscores the urgent need for effective strategies to combat the disease.