Rates of aging-related comorbidities, which require targeted medications to treat, have been shown to be increased among persons living with HIV compared with uninfected counterparts. Polypharmacy is generally defined as the concurrent use of 5 or more medications. We investigated polypharmacy prevalence for non-HIV medications over a 12-year period among HIV-positive and -negative participants in the Multicenter AIDS Cohort Study. Information regarding non-HIV medication use, HIV status, age, race/ethnicity, enrollment period, and medication insurance was obtained on 3,160 participants from semiannual visits between 2004 and 2016. Polypharmacy was defined as taking 5 or more non-HIV medications since the last health care visit. Generalized estimating equation models with repeated measures were produced overall and by HIV status to examine polypharmacy. The unadjusted prevalence of polypharmacy across all study visits was 18.6% and was higher among HIV-positive participants (24.4%) compared with HIV-negative participants (11.6%) (P < .0001). Among the 50 years and older age group, HIV-positive and HIV-negative participants had increases in polypharmacy over the observation period, from 38.4% to 46.8% (P = .0081) and from 16.7% to 46.0% (P < .0001), respectively. Among participants younger than 50, polypharmacy among HIV-positive participants remained stable (18.9% in 2004 to 17.3% in 2016; P = .5374) but increased among HIV-negative men (5.6% to 20.4%; P < .0001). After adjusting for age, race/ethnicity, and medication insurance, HIV-positive participants had a higher prevalence of polypharmacy than HIV-negative participants (25.3% vs 18.7%; P < .0001). Older age, white race, and having medication insurance coverage were also associated with greater polypharmacy. A convergence of polypharmacy prevalence was observed between HIV-positive and -negative participants at the end of observation. HIV-positive status was associated with an increased likelihood of polypharmacy, after adjusting for age, race/ethnicity, enrollment period, medication insurance, and study visit. Over time, polypharmacy prevalence increased among all participants, with converging rates between HIV-positive and -negative participants by the end of the observation period.