The purpose of this study was to explore factors associated with venous thromboembolism (VTE) among a cohort of HIV-infected patients and to describe early outcomes of warfarin anticoagulation therapy treated in a pharmacist-based anticoagulation clinic (ACC). A nested case-control study was conducted using the University of Alabama at Birmingham 1917 HIV Clinic Cohort. Conditional logistic regression was used to estimate factors associated with VTE. Among HIV-infected VTE cases, ACC-managed patients were compared to primary care provider (PCP)-managed patients to determine Time within Therapeutic INR Range (TTR). CD4 < 200 cells/µl (OR = 4.50; 95% CI = 1.52, 13.37; p = 0.007) and prior surgical procedures (13.20; 1.56; 111.4; p = 0.018) demonstrated positive associations with VTE, whereas longer HIV duration demonstrated a negative association (0.87; 0.78, 0.98; p = 0.019). TTR was 56.2% among ACC-managed patients compared to 30.5% of PCP-managed patients (p = 0.174). Overall, prior surgical procedures and low CD4 count were associated with an increased risk of VTE among HIV-infected patients. Despite small sample size, patients managed in ACC tend to achieve greater proportion of TTR compared to those managed by PCPs, suggesting that this model of therapy may provide additional benefits to HIV-infected patients.