The effect of hospital participation in the Japan Nosocomial Infection Surveillance (JANIS) programme on surgical site infection (SSI) prevention is unknown. To determine if participation in the JANIS programme improved hospital performance in SSI prevention. This retrospective before-after study analysed Japanese acute care hospitals that joined the SSI component of the JANIS programme in 2013 or 2014. The study participants comprised patients who had undergone surgeries targeted for SSI surveillance at JANIS hospitals between 2012 and 2017. Exposure was defined as the receipt of an annual feedback report 1 year after participation in the JANIS programme. The changes in standardized infection ratio (SIR) from 1 year before to 3 years after exposure were calculated for 12 operative procedures: appendectomy, liver resection, cardiac surgery, cholecystectomy, colon surgery, caesarean section, spinal fusion, open reduction of long bone fracture, distal gastrectomy, total gastrectomy, rectal surgery, and small bowel surgery. Logistic regression models were used to analyse the association of each post-exposure year with the occurrence of SSI. In total, 157,343 surgeries at 319 hospitals were analysed. SIR values declined after participation in the JANIS programme for procedures such as liver resection and cardiac surgery. Participation in the JANIS programme was significantly associated with reduced SIR for several procedures, especially after 3 years. The odds ratios in the third post-exposure year (reference: pre-exposure year) were 0.86 [95% confidence interval (CI) 0.79-0.84] for colon surgery, 0.72 (95% CI 0.56-0.92) for distal gastrectomy, and 0.77 (95% CI 0.59-0.99) for total gastrectomy. Participation in the JANIS programme was associated with improved SSI prevention performance in several procedures in Japanese hospitals after 3 years.