Background Nevirapine is used in many developing countries for the management of HIV-1 patients. Despite its usefulness, hypersensitivity reaction is a common complication that accounts for patients defaulting during therapy in Ghana. Genetic variations in drug-metabolizing enzymes have been implicated in reported adverse drug reactions observed in patients on nevirapine regimen. The study determined genotypic frequencies of specific CYP2B6 and SULT1A1 variants and their association with nevirapine hypersensitivity among persons living with HIV in the Ghanaian population.Methods An unmatched case-control study was conducted in a tertiary health facility in Ghana. Baseline clinical data were recorded from the patients’ folder. Genomic DNA (gDNA) samples were genotyped for CYP2B6*18 (c.983T > C) and SULT1A1*2 (c.638G > A) using Polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP).Results Mean age of the patients was 38 ± 9.47 years with the majority 77.1% (54/70) of the participants being females. For CYP2B6*18 (c.983T > C) genotype frequencies, T/T and T/C were 94.3% (66/70) and 5.7% (4/70) respectively while for SULT1A1*2 (c.638G > A) genotype frequencies, G/G, G/A, and A/A were 61.4% (43/70), 34.3% (24/70) and 4.3% (3/70) respectively. The prevalence of CYP2B6*18 (c.983T > C) and SULT1A1*2 (c.638G > A) minor allele were 2.9% (4/140) and 21.4% (30/140) respectively among the study participants.Conclusion Extensive metabolizer genotypes for CYP2B6*18 (c.983T > C) and SULT1A1*2 (c.638G > A) were more common than the intermediate and poor metabolizer genotype. However, CYP2B6 983C/C representing poor metabolizers of CYP2B6*18 (c.983T > C) were not detected among the study population. Genetic polymorphism of CYP2B6*18 (c.983T > C) and SULT1A1*2 (c.638G > A) were not associated with nevirapine hypersensitivity. However, these variants may contribute to differential variations of other drug responses among the Ghanaian population.