In Taiwan, an outbreak of acute hepatitis A (AHA) infection has been identified since June 2015. Approximately half of the cases occurred in HIV-infected men who have sex with men (MSM). We used the Taiwan Centers for Disease Control (TCDC)-operated National Disease Surveillance Systems (NDSS) to identify the incidence of AHA during 2011-2016. Between June 2015 and December 2016, a total of 1268 AHA cases were documented, and 601 cases (47.4%) were co-infected with HIV; the majority of whom were MSM (98.4%). Each AHA case was matched to two HIV-infected controls without AHA reported in the NDSS on age (± 5years), risk factor of HIV infection, HIV diagnosis date (± 30days) and county/city of residence at HIV diagnosis. Three hundred forty-three HIV/AHA cases were matched to 686 controls. In multivariable conditional logistic regression analysis, a previous gonorrhoea (adjusted OR=1.77, 95% CI 1.16-2.70) and recent (aOR=6.77, 95% CI 4.34-10.55) or remote syphilis report (aOR=3.56, 95% CI 2.48-5.13) were independently associated with AHA. The epidemic persisted till December 2016, and the cases with a new diagnosis of HIV infection after AHA (28/301, 9.3%) increased after July 2016 (P=.001). HIV/AHA cases were centralized in northern and central metropolitan areas and HIV-infected MSM with a recent history of sexually transmitted diseases in Taiwan. We recommend surveillance of associated behavioural and virologic characteristics and HAV counselling and testing for HIV-infected men.