The association between heavy rainfall and infectious intestinal diseases (IID) has not been well described and little research has been conducted in developing countries. This study examines the association between heavy rainfall and hospital admissions for IID in Ho Chi Minh City, the most populous city in Vietnam. An interrupted time-series method was used to examine the effect of each individual heavy rainfall event (HRE) on IID. The percentage changes in post-HRE level and trends of IID were estimated for 30 days following each HRE. Then a random-effect meta-analysis was used to quantify the pooled estimate of effect sizes of all HREs on IID. The pooled estimates were calculated over a 21 day lag period. The effects of a HRE on IID varied across individual HREs. The pooled estimates indicate that the levels of IID following a HRE increased from 7.3% to 13.5% for lags from 0 to 21 days, however statistically significant increases were only observed for lags from 4 to 6 days (13.5%, 95%CI: 1.4–25.4; 13.3%, 95%CI: 1.5–25.0; and 12.9%, 95%CI: 1.6–24.1 respectively). An average decrease of 0.11% (95%CI: − 0.55–0.33) per day was observed for the post-HRE trend. This finding has important implications for the projected impacts on residents living in this city which is highly vulnerable to increased heavy rainfall associated with climate change. Adaptation and intervention programs should be developed to prevent this additional burden of disease and to protect residents from the adverse impacts of extreme weather events.