With Captain Douglas N. Syverson in command, Hunley sailed 25 July 1962 for shakedown training off Cuba until 6 September 1962.
She visited several Gulf and Atlantic ports and returned to Norfolk 28 September for post-shakedown alterations until 8 December 1962.
After which the Hunley paid a 3-day visit to New York City to host the Naval Reserve Officers Seminar "New Ships for the Modern Navy".
She departed from the Norfolk Operating Base 29 December 1962 for Holy Loch, Scotland, arriving 9 January 1963.
Almost immediately she began taking the load off USS Proteus, whom she officially relieved 15 March 1963 as tender to Submarine Squadron 14 at Holy Loch.
This duty continued until 12 April 1964 when Hunley sailed for conversion that provided capability of handling the new A3 Polaris Missile.
She resumed her duties at Holy Loch on 15 June 1964.

A Polaris milestone was reached in December 1965 when USS Thomas A. Edison came alongside to commence the 100th refit of a nuclear ballistic submarine (SSBN) by the Hunley.
This signified that one hundred SSBN submarines had gone out on time from Hunley and not one of them had to make an early return from patrol.
This represented some 200 months of Polaris on station or 16½ years of submerged strategic deterrent since Hunley's arrival in Holy Loch 9 January 1963.
Hunley's motto was "We Serve to Preserve Peace".
Hunley returned to the United States late in 1966 and in 1967 operated out of Charleston, South Carolina.
Hunley put out for Guam on the day after Christmas, 1967, to relieve Proteus at Polaris Point from January to June 1968 while Proteus underwent a self-overhaul, with Hunley returning to Charleston in July 1968.
  In 1971 Hunley relieved Proteus in Guam again in order for Proteus to go to shipyard.
 It was while Hunley was in Guam that the Machinery Repair Division received the Meritorious Unit Commendation, having expended 4500 hours of repair labor on various units of the U.S. Pacific Fleet.
 In 1973 Hunley returned to Bremerton Shipyard for conversion overhaul.
 After completion Hunley returned to Charleston, South Carolina, to again service the Atlantic Fleet.
In 1978, "Hunley" went to Boston Naval Shipyard for hull cleaning and hull valve repairs in preparation for relieving "Proteus" once again in Guam.
In transit to Guam, "Hunley" went around South America rather than through the Panama Canal.
In 1980, "Hunley" was relieved by "Proteus" and returned to Charleston via the Panama Canal.

Hunley was decommissioned on 30 September 1994 and struck from the Naval Vessel Register on 3 May 1995 and turned over to the Maritime Commission on 1 May 1999.
Hunley was subsequently sold to the Southern Scrap Materials Company on 5 January 2007 for scrapping.
With Captain Douglas N. Syverson in command, Hunley sailed 25 July 1962 for shakedown training off Cuba until 6 September 1962. She visited several Gulf and Atlantic ports and returned to Norfolk 28 September for post-shakedown alterations until 8 December 1962. After which the Hunley paid a 3-day visit to New York City to host the Naval Reserve Officers Seminar "New Ships for the Modern Navy". She departed from the Norfolk Operating Base 29 December 1962 for Holy Loch, Scotland, arriving 9 January 1963. Almost immediately she began taking the load off USS Proteus, whom she officially relieved 15 March 1963 as tender to Submarine Squadron 14 at Holy Loch. This duty continued until 12 April 1964 when Hunley sailed for conversion that provided capability of handling the new A3 Polaris Missile. She resumed her duties at Holy Loch on 15 June 1964.
A Polaris milestone was reached in December 1965 when USS Thomas A. Edison came alongside to commence the 100th refit of a nuclear ballistic submarine (SSBN) by the Hunley. This signified that one hundred SSBN submarines had gone out on time from Hunley and not one of them had to make an early return from patrol. This represented some 200 months of Polaris on station or 16½ years of submerged strategic deterrent since Hunley's arrival in Holy Loch 9 January 1963. Hunley's motto was "We Serve to Preserve Peace". Hunley returned to the United States late in 1966 and in 1967 operated out of Charleston, South Carolina. Hunley put out for Guam on the day after Christmas, 1967, to relieve Proteus at Polaris Point from January to June 1968 while Proteus underwent a self-overhaul, with Hunley returning to Charleston in July 1968.   In 1971 Hunley relieved Proteus in Guam again in order for Proteus to go to shipyard.  It was while Hunley was in Guam that the Machinery Repair Division received the Meritorious Unit Commendation, having expended 4500 hours of repair labor on various units of the U.S. Pacific Fleet.  In 1973 Hunley returned to Bremerton Shipyard for conversion overhaul.  After completion Hunley returned to Charleston, South Carolina, to again service the Atlantic Fleet. In 1978, "Hunley" went to Boston Naval Shipyard for hull cleaning and hull valve repairs in preparation for relieving "Proteus" once again in Guam. In transit to Guam, "Hunley" went around South America rather than through the Panama Canal. In 1980, "Hunley" was relieved by "Proteus" and returned to Charleston via the Panama Canal. 
Hunley was decommissioned on 30 September 1994 and struck from the Naval Vessel Register on 3 May 1995 and turned over to the Maritime Commission on 1 May 1999. Hunley was subsequently sold to the Southern Scrap Materials Company on 5 January 2007 for scrapping.
USS Hunley (AS-31)