Porcine delta coronavirus (PDCoV) has been reported in many countries, including the United States, Canada, South Korea, China, Thailand, Vietnam and Laos. In December 2016, clinical diarrhea similar to that caused by porcine epidemic diarrhea virus (PEDV), but with a lower mortality rate, was reported on a swine farm in Shanghai, China. 6 Intestine samples were collected from dead suckling piglets (<3 weeks old) with clinical diarrhea, and they were assayed for the presence of swine enteric coronaviruses. Polymerase chain reaction results were positive for PDCoV (6/6), but negative for PEDV (0/6), transmissible gastroenteritis virus (TGEV) (0/6) and porcine rotavirus group A (Rota A) (0/6). The full-length genome sequence of the PDCoV strain SHJS/SL/2016 was determined. Phylogenetic trees demonstrated that PDCoV strain SHJS/SL/2016 belongs to the Chinese clade, which might share a common evolutionary ancestor with United States and South Korean clades, but it clustered separately from Thai and Laotian PDCoV strains. This report describes the complete genome sequence of SHJS/SL/2016, and the data will promote a better understanding of the molecular epidemiology and genetic diversity of PDCoV isolates in China.