Hepatitis E virus (HEV) is an important public health concern in the world, especially in developing countries of Africa and Asia, including China. Hepatitis E is recognized as a zoonotic disease, which is transmitted across species, including between humans and swine. HEV is highly endemic in China, but the complete sequence of HEV in southwestern China is lacking. Swine HEV strain KM01 was isolated from a village in rural Kunming, Yunnan province, China, where swine are housed with humans. Here, we report the complete genome sequence of the swine HEV strain KM01. The sequence and phylogenetic analyses reveal that swine HEV is closely related to the strain isolated from Xinjiang (CHN-XJ-SW13). The genome of the KM01 strain will facilitate further study of HEV molecular epidemiology and genetic diversity in China.