The history of the San Juan area goes back to pre-Incan time. There are stone foundations of pre-Incan origin on the north side of the Chorunga River that have been identified by archeologists. The gold of the area is said to be known by the Incas and some of the gold obtained by the Spanish conquistadors is said to have been mined by the Incas in the San Juan area.

The area has been mined by various mining groups since the early 1900s using primitive methods, but it was not until the early 1970s that the owners installed a mill using cyanide and zinc precipitation. The original small mill was built-up gradually with the addition of ball mills.  The nominal capacity was increased to 700 tonnes per day. According to government records, San Juan has produced a total of 1.2 million ounces of gold to date.

The San Juan property was purchased by Century Mining in May 2006. Century Mining now owns 82.6% of the property through two subsidiaries, and is currently expanding production with the objective of paying the carrying costs while planning, drilling and development work is being carried out to place the mine on a profitable footing again.