BACKGROUND: The effect of antiretroviral therapy (ART) on the natural history of anal HR-HPV and anal lesion progression is not well established. We reviewed the association of ART and other HIV-related factors on anal HPV infection, anal intraepithelial neoplasia (AIN), and anal cancer among people living with HIV (PLHIV). METHODS: We searched Medline and Embase for studies from 1 January 1996 to 30 October 2019 that reported the association of HIV-related exposures (ART, HIV-RNA plasma viral load [PVL] and nadir or current CD4+ cell count) with outcomes of anal HR-HPV prevalence, incidence or persistence or prevalence, incidence, progression or regression of anal histological/cytological abnormalities, or anal cancer incidence. We assessed the risk of bias of included studies using the Newcastle-Ottawa scale. We performed random-effects meta-analyses; heterogeneity was examined using I 2 statistic. FINDINGS: 122 studies were included comprising 417,006 PLHIV (19%, 44% and 5% women, men-whohave-sex-with-men; men-who-have-sex-with-women, respectively; 32% of studies did not stratify findings by gender and/or sexual orientation). PLHIV taking ART had 35% lower HR-HPV prevalence compared to ART-naïve (crude Odds Ratio[cOR]=0.65, 95%CI:0.54-0.79; I 2 =12.1%) in 18 studies and prolonged ART use was associated with a 10% reduction in HR-HPV prevalence in two studies (per year: aOR=0.90, 95%CI:0.85-0.95, I 2 =0.0%). PLHIV with undetectable PVL had lower HSIL/AIN2+ prevalence compared to those without (cOR=0.84, 95%CI:0.72-0.98, I 2 =0.0%) in 16 studies, particularly if sustained for >1 year (cOR=0.62, 95%CI:0.47-0.81, I 2 =0.0%). ART was not associated with anal cancer incidence when adjusted for years living with HIV in 3 studies (aHR=1.11, 95%CI: 0.68-1.80, I 2 =0.0%), but ART users with sustained undetectable HIV PVL had 44% lower risk of anal cancer compared to those without (aHR=0.56, 95%CI:0.44-0.70, I 2 =0%) and for each 100 cells/µl increase in nadir CD4+ count, there was a 40% decrease in anal cancer incidence (cHR=0.60, 95%CI:0.46-0.78, I 2 =21.7%). INTERPRETATION: Effective ART use and early initiation at higher nadir CD4+ may reduce anal HR-HPV and anal cancer risk.