Malaria is a life-threatening disease caused by protozoan Plasmodium species. Plasmodium falciparum is the deadliest species. Reducing and eliminating malaria burden are linked to most of the Sustainable Development Goals (SDG), central to SDG3 targeting the end of malaria by 2030. This study was aimed at assessing the Management of malaria and prevalence of P. falciparum kelch-13 among febrile patients in selected Government Hospitals in Nigeria. Malaria patients (399) attending outpatient clinics of the Hospitals between August, 2019 and January, 2021, were enlisted in the study, following ethical approval and informed consents. Blood (5mL) was collected from patients for microscopic and molecular investigation of malaria parasite. DNA extraction, PCR amplification, BLAST, and alignment were performed. Plasmodium resistance to Artemether/lumefantrine was determined by PCR amplification of extracted DNA using Kelch-13 gene primer. Data obtained were subjected to One-way Analysis of Variance and Linear Regression. The VapA gene primer amplified 55 (68.75%) out of the 80 DNA extracts tested. Twenty-five strains of P. falciparum belonging to 3 clades phylogenetically were identified and they showed evolutionary relationships with others. Plasmodium falciparum resistant Kelch-13 gene was detected in 70% of the isolates. This study observed a high prevalence of resistant gene to ACT drugs in the study area. Monitoring the effectiveness of ACTs must be done routinely to ensure timely changes in National treatment policies.