Background: Malaria, caused by a protozoan parasite of the genus Plasmodium and highly endemic in Sub-Saharan Africa, continues to be a significant public health challenge in Nigeria, particularly among children and pregnant women, though it affects all age groups. Despite ongoing efforts to curb malaria, the parasite remains a global health issue, posing persistent challenges to people and healthcare systems in endemic regions. Method: This study employed a retrospective descriptive survey to assess malaria prevalence between January 2020 and December 2022. A total of 28,077 hospital records were analysed, encompassing 9,901 from AMAC, 5,394 from Kuje, 5,275 from Abaji, 1,601 from Kwali, 4,793 from Bwari, and 1,113 from Zuba, all within the Federal Capital Territory, over the three-year period. Result: This study revealed a total malaria prevalence of 37.2% from 2020 to 2022 across major hospitals in the six area councils of the Federal Capital Territory (FCT). The highest prevalence was observed in Wuse (46.2%) and the lowest in Bwari (26.5%). Yearly prevalence peaked in 2021 (41%), followed by 2022 (36%) and 2020 (32%). Malaria prevalence showed seasonal peaks, particularly in June and August, with variations across the regions. Age-dependent analysis indicated the highest prevalence among children aged 0-5 years, while pregnant women exhibited a 58.1% prevalence, with significant regional differences, particularly in Wuse (77.3%) and Kwali (63.7%). Statistical analysis highlighted significant differences in prevalence across regions between 2021 and 2022 (p<0.0347) and in pregnant women across regions (p=0.0035), though yearly trends were not statistically significant (p=0.075). Conclusion: This study underscores malaria's ongoing impact as a critical public health concern in the Federal Capital Territory (FCT) of Nigeria, revealing significant variations in prevalence across different regions, age groups, and seasons between 2020 and 2022. This study highlights the continued susceptibility of children under five to malaria and the disease's pronounced seasonal patterns, especially during the rainy months.