Human papillomavirus (HPV) coinfection remains common globally. However, its clinical significance compared to mono-infection remains controversial. Further, the epidemiology of HPV genotype combination in coinfection is not well studied in Kenya. . Between June and August 2023, a cross-sectional facility-based survey enrolled 434 women aged 16–68 years using purposive sampling strategy. Structured questionnaire was obtained from each woman regarding demographic and sexual behavior characteristics. Cervical specimen was collected from each participant and analyzed using RIATOL assay to determine HPV genotypes and viral load. Overall, HPV 52 was the most frequently detected HPV strain. The mean HPV viral load was elevated among coinfected women than those with mono-infection but there was no evidence to support differences in viral load in the two groups (P = 0.113). Mono-infection was common (58.52%). HPV 16 was noted to have a near equal presence both in mono-infection and coinfection (52.17% and 47. 83%), respectively. HPV 33 (alpha 9) and 45 (alpha 7) had the greatest preference for each other compared to all other HPV interactions. HPV 52 is the most prevalent HPV in the population supporting the need for the nonavalent HPV vaccine. Mono-infection with HPV 16 remains common corroborating the relevance of bivalent vaccine in resource limited setting where nonavalent vaccines may be unavailable. The frequent coinfection preference of HPV 33 and 45 (alpha 9 and alpha 7, respectively) pauses the need for further concurrent characterization. HPV vaccination and education on safe sexual behaviors is key in reducing HPV coinfection.