This study aims to estimate the prevalence of HIV among each of the three key populations in Vietnam: people who inject drugs (PWID), female sex workers (FSW), and men who have sex with men (MSM) and quantify their shared risk factors for HIV infection through a systematic review and meta-analysis of recent literature (published in 2001–2017) in the relevant topics. A total of 17 studies consisting of 16,304 participants were selected in this review. The meta-analysis results revealed that the pooled prevalence estimates with 95% confidence intervals (CIs) among PWID, FSW, and MSM were: 0.293 (0.164, 0.421), 0.075 (0.060, 0.089), and 0.085 (0.044, 0.126), respectively. The findings also indicated that injecting drug use (OR: 9.88, 95%CI: 4.47–15.28), multiperson use of injecting equipment (OR: 2.91, 95%CI: 1.69, 4.17), and inconsistent condom use (OR: 2.11, 95%CI: 1.33, 2.90) were the shared risk factors for HIV infection among these population groups. The findings highlighted the importance of HIV prevention approaches to addressing the shared sexual and drug-related practices among the key populations in consideration of their overlapping social networks.