CYP2B6 one of the most polymorphic enzymes, plays a major role in the metabolism of artemisinin and its derivatives. Variation in the frequency of the most common yet functionally deficient allele may impact artemisinin exposure, potentially contributing to differences in treatment outcomes This study assessed the prevalence of the genotype among patients with uncomplicated malaria treated with artemether-lumefantrine at Adjumani District Hospital in the West Nile region, Uganda. A total of 100 randomly selected patients with microscopically confirmed uncomplicated malaria receiving artemether-lumefantrine (AL) were included in the study. Blood samples, 2-3 mL each, were collected using EDTA tubes on days 0 and 3 after AL administration. DNA was extracted using Qiagen DNA Mini kit. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) was used to determine the genotype of the participants. positivity was determined by microscopy and qPCR. For qPCR, parasite clearance was determined using comparative CT value. Data analysis was done using STATA 17.0 at a 95% significance level. Among the malaria patients genotyped, 65% were female, and 35% were male, with a mean age of 17±10 years. The variant allele frequency was 0.37, and the genotype frequency was 43% GG, 17% TT and 40% GT. day 3 microscopy positivity was 14% (6/43) among the GG, 37.5% (15/40) among the GT, and 17.64% (3/17) among the TT patients. PCR positivity rates were 58.1% (25/43) in the GG, 72.5% (29/40) in the GT, and 52.9% (9/17) in the TT patients. Heterozygous individuals (GT) had slow parasite clearance by a 10-fold difference compared to the homozygous (GG, TT) individuals (=323.0; =-2.3442; =0.019). Malaria patients in Adjumani district had a high frequency of the variant allele. Interindividual variability in clearance exists, with heterozygous patients demonstrating slow artemether-lumefantrine parasite clearance. There is a need to consider incorporating host genomic factors, such as metabolising enzyme genotype into routine Therapeutic Efficacy Studies (TES).