Anal human papillomavirus (HPV) prevalence is increasing; therefore, this study investigated the anal HPV and associated factors; and further, investigated anal-cervical HPV concordance and associated factors among women of Eastern Cape Province, South Africa. A total of 326 women aged 18–60 were recruited from an Eastern Cape community health facility. HPV DNA was detected in cervical and anal specimens using the Seegene Anyplex™ and Allplex™ II HPV28 assay respectively. Anal HPV was detected in 68.1% and a proportion of 38.7% had ≥1 HPV type(s) covered by the Gardasil ®9 HPV vaccine. Anal HPV infection was significantly associated with cervical HPV infection (RR: 1.46, 95% CI: 1.22–1.80, p<0.0001) and abnormal cervical cytology (RR: 1.45, 95% CI: 1.24-1.62, p<0.0001). The risk of anal HPV infection was decresed among married (RR:0.80, 95% CI: 0.62-0.98, p=0.041) and once pregnant women (RR: 0.78, 95% CI:0.68-0.94, p=0.015). It was also decreased among those wiping in any direction after peeing or bowel movement than those who wipe from vagina-to-anus (RR: 0.68, 95% CI: 0.45-0.94, p=0.018) or from anus-to-vagina (RR: 0.66, 95% CI: 0.44-0.90, p=0.006). Anal-cervical concordance was observed in 33.5% and it was associated with abnormal cervical cytology (RR: 2.81, 95% CI: 2.12-3.60, p<0.0001), drinking alcohol (RR: 2.01, 95% CI: 1.36-2.91, p=0.001) and increased new sexual partners past 12-months (RR: 1.42, 95% CI: 1.02-1.92, p=0.040). High anal HPV prevalence and anal-cervical HPV type concordance was observed among Eastern Cape women. Understanding anal HPV and associated factors can contribute to strategies towards anal HPV and cancer prevention.