The association between physical activity (PA), degree of insulin resistance (IR), and HIV infection is unclear. We hypothesized that PA might differentially affect the degree of IR through the direct and indirect influences of HIV, antiretroviral medications, and sociodemographic characteristics. The International Physical Activity Questionnaire (IPAQ) was administered to Multicenter AIDS Cohort Study (MACS) participants from 4/2010 to 3/2011 to generate metabolic equivalents (METs) total score and PA category. We determined the concurrent homeostatic model assessment IR (mmol/liter) (HOMA-IR) value from fasting glucose and insulin. We examined the HIV-PA relationship using quantile regression and the HIV-PA-HOMA-IR value relationship using linear regression. Among the 1,281 men, the proportions of men in the low (25% in HIV(+) vs. 23% in HIV(-)), moderate (26% vs. 27%), and high (49% vs. 49%) PA categories were similar by HIV status. The HOMA-IR value was higher among the HIV(+) men (p<0.001), and both HIV infection and low PA were associated with a higher degree of IR (p<0.0001 and p=0.0007). However, the PA-HOMA-IR value interaction was not different by HIV status. The HOMA-IR value was higher among HIV(+) men although the PA was similar. It is unknown if more exercise will overcome the metabolic derangements associated with HIV and its treatment.