HIV/AIDS is a known risk factor for the development of pulmonary tuberculosis (PTB). However, the association is less clear between HIV and extrapulmonary tuberculosis (EPTB). We conducted a systematic review to determine the association between HIV and EPTB. We searched the electronic databases Medline, Embase, and relevant conference literature using defined search terms for EPTB and HIV. Only publications in English and only studies reporting adjusted estimates were included, while our search criteria did not include restriction by age or geographic location of study participants. Qualitative and quantitative analyses (including I (2) test for heterogeneity) were performed. Sixteen studies (15 cross-sectional and 1 case-control) conducted from 1984 to 2016 were included in the final analyses after screening 5163 articles and conference abstracts. Our qualitative analysis showed heterogeneity in study design and study population characteristics along with a medium/high risk of bias in the majority of studies. While most of the individual studies showed increased odds of EPTB compared with PTB among HIV-infected individuals, we did not provide an overall pooled estimate, as the I (2) value was high at 93% for the cross-sectional studies. While an association between HIV and EPTB is observed in most individual studies, the high heterogeneity and risk of bias in these studies highlight the need for further well-designed prospective cohort studies to assess the true risk of EPTB in the HIV-infected patient population.