On 15 November 2017, San Juan went missing during a routine patrol in the South Atlantic off the coast of Argentina, believed to have suffered an electrical malfunction, and a multi-nation search operation was mounted. Within hours of San Juan's last transmission, an acoustic anomaly consistent with an implosion was detected in the vicinity of the vessel's last known location. On 30 November, the search and rescue operation was abandoned.
The Argentine Navy reported on 16 November 2018 that the wreck of San Juan had been found at a depth of 907 metres (2,976 ft), 460 kilometres (290 mi) southeast of Comodoro Rivadavia. The submarine’s imploded wreckage was strewn over an area of 8,000 square metres (86,000 sq ft).