Background We investigated safety-related outcomes of hepatobiliary pancreatic (HBP) surgeries performed after establishment of the Japanese Society of HepatoBiliary-Pancreatic Surgery (JSHBPS) board certification system for expert surgeons. Methods We analyzed post-HBP surgery mortality data obtained from annual safety reports provided by board-certified training institutions between 2012 and 2015.Results The 90-day mortality rate for the 53,929 high-level HBP surgeries performed at board-certified training institutions was 1.7%. The 30-day mortality rates for 2012, 2013, 2014, and 2015 were 0.9%, 0.7%, 0.6%, and 0.6%, respectively, and the 90-day mortality rates were 2.1%, 1.8%, 1.6%, and 1.3%, respectively, with significant decreases in both. The surgeries with high 4-year cumulative mortality rates were left hepatic trisectionectomy (10.3%), hepatopancreatectomy (7.6%), liver transplant recipient surgery (6.7%), hepatectomy with extrahepatic bile duct resection (4.6%), and right hepatic trisectionectomy (4.5%). Over the 4-year period, the number of operations increased, but the 90-day mortality rates for these surgeries, with the exception of right trisectionectomy, decreased. Conclusions The JSHBPS board certification system for expert surgeons has significantly decreased mortality subsequent to high-level HBP surgeries. Reducing mortality associated with high-risk HBP surgeries will be our next challenge.