This article focuses on understanding how the Porcine Epidemic Diarrhea (PED) virus influenced the production efficiency of the swine industry in Taiwan. A total of 96 valid sample data were collected during March of 2014. The Data Envelopment Analysis (DEA) was adopted to evaluate production efficiency before, and after, the PED events. Results show that the PED events in Taiwan had weakened overall technical efficiency about 8.6%. Large scale farms, older farms, and farms in the Central area appeared to be the most heavily impacted. Lastly, the percentage change in production efficiency in the DEA estimation are very close to the percentage changes in inventory on farms reported by government. This supports our estimation of efficiency lost by the DEA practically.