While studies have examined the association between weather variables and acute diarrhea in a city, region, or country, less evidence is available on the temperature effect across countries. The objective of this study is to elucidate the nonlinear and lagged association between ambient temperature and acute diarrhea in Hong Kong, Taiwan, and Japan. We collected weekly surveillance statistics on acute diarrhea with the corresponding meteorological data from 12 regions of Hong Kong, Taiwan, and Japan during 2012–2016. Firstly, we fitted the region-specific counts of acute diarrhea in a distributed lag nonlinear model (DLNM) which accounts for the non-linearity and lagged effect of temperature. Secondly, we applied meta-analysis to pool estimates across 12 regions. A total of 5,992,082 acute diarrhea cases were identified. We found that (1) the pooled overall cumulative relationship between the relative risk (RR) of acute diarrhea and temperature was the greatest (RR = 1.216; 95% CI: 1.083, 1.364) at 11 °C; (2) a pooled predictor-specific summary association at lower temperatures (12 °C or 25th percentile) began immediately and vanished after four weeks. Predictions and error analysis for new onsets of acute diarrhea in 2017 were evaluated. An early warning system based on the information of temperature variation was suggested for acute diarrhea control management.