Assessing the risk of vaccines is essentially a scientific issue. However, a court’s interpretation of scientific knowledge is not necessarily the same as that of scientists, especially in uncertain cases involving new vaccines or rare side effects. In 2017, the Supreme Administrative Court in Taiwan confirmed a disputed causal relationship between an H1N1 vaccine and a case of acute disseminated encephalomyelitis in a teenage boy, in contrast to all medical experts who disagreed with this judgment. The interplay between law and science might be complicated when scientific knowledge is incomplete. A court’s interpretation of scientific knowledge could diverge from experts’ consensus because the purpose of judicial investigations differs from that of scientific investigations. After this case, the Taiwanese government revised vaccine compensation regulations, incorporating more specific criteria recommended by the World Health Organization. The revised regulations can enable judges to better understand and check medical experts’ conclusions and reasoning processes. This case is a good model to help other countries minimize systematic conflicts between law and science in recognizing risks.