The contract to build SSN 751 was awarded on November 30, 1982, and her keel was laid on August 9, 1985. She was launched on December 6, 1986, and commissioned on August 6, 1988, with Cmdr. Charles Young in command.

USS San Juan was the first Los Angeles-class submarine to receive a number of significant improvements to the class's basic design, creating the 688I-class ("I" for "improved"). SSN 751 and all following submarines in her class are quieter, incorporate an advanced AN/BSY-1 "busy one" combat control system/sonar suite, and have dedicated tubes for vertical launch of the Tomahawk cruise missile. The externally visible changes are also significant, as the San Juan had her forward diving planes moved from the sail to the bow and made retractable. Together, the retractable bow planes, strengthening of the sail, and installation of additional depth control and support systems make it possible for San Juan to break through polar and near-polar ice as a part of 'normal' ship operations.

On March 19, 1998, USS San Juan collided with USS Kentucky (SSBN 737) south of Long Island, New York. The balistic-missile submarine suffered damage to its rudder but no injuries occurred on either ship; the San Juan's forward ballast tank was breached, but the ship was able to surface and return to port.

January 18, SSN 751 arrived in Aksaz Naval Base for a week-long port visit Marmaris, Turkey, and to get tender support services from USS Emory S. Land (AS 39).

February 21, The San Juan moored outboard the USS Emory S. Land while at anchor off Souda Bay, Crete, for a two-day port call.

March 21, The Los Angeles-class attack submarine recently launched its first Tomahawk Land Attack Missiles (TLAMs), from the station in the Red Sea, in support of Operation Iraqi Freedom.

March 31, SSN 751 pulled again into Souda Bay for a five-day Fleet Maintenance Availability (FMAV).

April 23, USS San Juan returned to Naval Submarine Base New London after an extende combat deployment in the U.S. 5th and 6th Fleet AoR.

April 27, 2004 Cmdr. Harvey L. Guffey relieved Cmdr. Edward L. Takesuye as commanding officer of USS San Juan in a ceremony at Shepherd of the Sea Chapel.

June 16, The San Juan moored outboard the USS Emory S. Land in La Maddalena, Italy, for a week-long FMAV. SSN 751 recently departed for a scheduled deployment in support of the Global War on Terrorism.

August 13, SSN 751 recently pulled into Manama, Bahrain, for a 10-day upkeep.

October 18, The Los Angeles-Improved class attack submarine arrived in Souda Bay, Crete, for a brief port call.

July 3, 2006 USS San Juan fired the Mark 48 torpedo that deliberately sank the USNS Butte in a target exercise. She is also a primary testing platform for new, advanced systems being developed by the U.S. Navy.

March 13, 2007 SSN 751 was the subject of a search & rescue mission by elements of the Enterprise Carrier Strike Group when a red flare was spotted in her projected vicinity, suggesting an emergency. Communications were established by the early hours of the next day (the San Juan had been submerged) and no problems were indicated.

May 22, USS San Juan pulled into Souda Bay, Crete, for a routine port visit. She departed her homeport of Groton, Conn., earlier this month for deployment in support of maritime operations.

March 26, 2008 The San Juan is currently in the Groton waterfront's dry dock undergoing a scheduled rehabilitation period.

March 6, 2009 Cmdr. Oliver T. Lewis relieved Cmdr. Mike Martin as CO of SSN 751 during a change-of-command ceremony at New London's Shepherd of the Sea chapel.

November 4, USS San Juan arrived in Simon's Town to participate in a series of first-ever, at-sea engagements with the South African Navy.

December 1, SSN 751 returned to NSB New London after a six-month deployment to the U.S. European (EUCOM) and African Command (AFRCIOM) areas of responsibility (AoRs). The submarine also visited Souda Bay, Greece; Diego Garcia; and Port Victoria, Seychelles.

April 8, 2010 USS San Juan arrived at Portsmouth Naval Shipyard in Kittery, Maine, for maintenance work and several system upgrades.

August 4, 2011 The Los Angeles-improved class attack submarine departed dry-dock one day earlier than scheduled.

February 10, 2012 USS San Juan returned to Naval Submarine Base New London after completing its Engineered Overhaul (EOH) at PNSY.

March 30, The San Juan moored at the Naval Ordnance Test Unit wharf in Port Canaveral, Fla., for a brief port call.

April 27, Cmdr. Joseph J. Biondi relieved Cmdr. Oliver T. Lewis as CO of the USS San Juan during a change-of-command ceremony aboard the sub at NSB New London.

May 11, Capt. Vernon J. Parks, Jr., relieved Capt. William R. Mertz as Commander, Submarine Development Squadron (COMSUBDEVRON) 12, during a change-of-command ceremony aboard the USS San Juan at NSB New London.

October 15, 2013 USS San Juan departed Groton for a scheduled Middle East deployment.

April 18, 2014 SSN 751 pulled into Souda Bay, Crete, Greece, for a routine port call.

May 16, USS San Juan returned to homeport after a seven-month deployment. Port calls to Lisbon, Portugal; Bahrain; Jebel Ali, United Arab Emirates; and Rota, Spain.

June 4, Capt. Vernon J. Parks, Jr., Commander, Submarine Development Squadron (SUBDEVRON) 12, relieved Cmdr. Joseph Biondi "due to a loss of confidence in his ability to serve effectively as commanding officer." Cmdr. Sam R. Geiger, deputy commander of Submarine Squadron (SUBRON) 4, assumed temporary command of the San Juan.

December 2, Cmdr. John D. Craddock relieved Cmdr. Sam R. Geiger as CO of the San Juan during a change-of-command ceremony at Dealey Center on Naval Submarine Base New London.

December 23, 2015 USS San Juan moored at Pier 2 on Naval Submarine Base New London after underway for routine training; Underway again on Dec. 28.

January 4, 2016 The San Juan made a brief stop off Groton for personnel transfer; Brief stop off Norfolk on Jan. 7; Moored at Berth 3, Pier 3 in Naval Station Norfolk from Jan. 11-12; Brief stop off Naval Station Norfolk on Jan. 14; Returned home on Jan. 19; Underway again on Jan. 26; Brief stop off Naval Station Norfolk on Feb. 1; Returned to Groton on Feb. 5.

February 14, The Los Angeles-improved class attack submarine departed homeport for a routine operations; Brief stop off Groton on Feb. 22; Brief stop off Naval Station Norfolk on Feb. 29 and March 3; Returned home on March 7.

March 2?, USS San Juan departed Groton for a scheduled North Atlantic deployment.

May 14, The San Juan moored at Haakonsvern Naval Base in Bergen, Norway, for a four-day port call; Brief stop west off Brensholmen, Norway, for a personnel transfer on May 31 and June 2.

June 8, SSN 751 moored at Her Majesty's Naval Base (HMNB) Clyde in Faslane, Scotland, for a three-day port call; Moored at HMNB Clyde again from July 18-28.

September 9, The San Juan moored at Berth 2, Pier 1 on Naval Station Rota, Spain, for a five-day port call.

September 23, USS San Juan moored at Pier 33S on Naval Submarine Base New London following a six-month deployment.

December 13, The San Juan made a brief stop off Naval Station Norfolk, Va., for personnel transfer; Brief stop off Groton on Dec. 15; Returned home on Dec. 1?.

February 3, 2017 USS San Juan returned to NSB New London after underway for routine operations; Underway again on Feb. ?; Brief stop off Groton on Feb. 11; Returned home on Feb. 13; Underway again from March 6-13.

April 21, Cmdr. Ravi M. Desai relieved Cmdr. John D. Craddock as CO of the San Juan during a change-of-command ceremony at Dealey Center on NSB New London.

April 28, The San Juan recently departed homeport for routine operations.?

May 22, USS San Juan moored at Trident Wharf in Port Canaveral, Fla., for a three-day port call.

October 2?, USS San Juan departed Groton for a scheduled North Atlantic deployment.

November 25, The San Juan moored at Her Majesty's Naval Base (HMNB) Clyde in Faslane, Scotland, for a week-long port call; Inport Faslane again from Dec. ?-22.

February 23, 2018 SSN 751 moored at HMNB Clyde in Faslane for a routine port call; Moored at Berth 2, Pier 1 on Naval Station Rota, Spain, for emergent repairs from March 28- April 4.?

April 27, USS San Juan moored at Pier 6N on Naval Submarine Base New London following a six-month deployment.

May 3, Capt. David A. Youtt relieved Capt. Oliver T. Lewis as Commander, Submarine Squadron (COMSUBRON) 12 during a change-of-command ceremony on board the San Juan.

May 24, Rear Adm. Leonard C. Dollaga relieved Rear Adm. James S. Pitts as Commander, Undersea Warfighting Development Center during a change-of-command ceremony on board the USS San Juan.

March 7, 2019 A sailor was found dead early Thursday morning in a locked space on a barge, housing crewmembers, while the USS San Juan was at the floating dry-dock Shippingport (ARDM 4) undergoing maintenance.

May 2, The San Juan recently moored at Pier 6N on Naval Submarine Base New London; Underway for sea trials on May ?; Moored at Trident Wharf in Port Canaveral, Fla., from May 24-28; Moored at Pier 17N on May 31.

August 16, Cmdr. Douglas R. Sattler, Jr., relieved Cmdr. Ravi M. Desai as CO of the San Juan, during a change-of-command ceremony on board the ex-USS Nautilus (SSN 571) on Naval Submarine Base New London.

September 9, USS San Juan moored at Pier 10S on Naval Submarine Base New London after underway for routine operations; Underway again on Sept. 19; Moored at Pier 17S on Oct. 1?.

June 3, 2020 The San Juan made a brief stop off Groton for personnel transfer; Brief stop off Groton again on June 5; Moored at Pier 31S on June 15.

August 6, The Los Angeles-improved class attack submarine made a brief stop off Groton for personnel transfer; Brief stop off Naval Station Norfolk on Aug. 14.

September 10, USS San Juan departed homeport to participate in anti-submarine warfare (ASW) exercise Black Widow, with the USS Wasp (LHD 1), USS Arleigh Burke (DDG 51), USS McFaul (DDG 74) and USS Colorado (SSN 788), off the U.S. East Coast from Sept 12-17; Brief stop off Groton for personnel transfer on Oct. 5.?

January ?, 2021 USS San Juan departed Groton for a scheduled deployment in the U.S. 6th Fleet Area of Responsibility (AoR).

March 11, The San Juan moored at Berth K14 in Souda Bay, Greece, for a brief stop after recently participated in anti-submarine warfare (ASW) exercise Dynamic Manta 2021; Brief stop off Limassol, Cyprus, for supplies on April 15; Moored at Berth 2, Pier 1 on Naval Station Rota, Spain, from May 8-15.

May 26, SSN 751 moored at Valiant Jetty on Her Majesty's Naval Base (HMNB) Clyde in Faslane, Scotland, for a two-week port call; Moored at Valiant Jetty again from Aug. 7-10.

August 24, USS San Juan moored at Pier 8S on Naval Submarine Base New London following a seven-month deployment.

October 1, The San Juan departed Naval Submarine Base New London for routine operations; Moored at Pier 17S on Oct. ?.

December 17, USS San Juan moored at Naval Submarine Base New London after underway for routine operations; Underway again on Jan. ?; Moored at Pier 31S on Jan. 28.

March 10, 2022 USS San Juan made a brief stop off the coast of Groton for personnel transfer.?

May 13, Cmdr. Alan T. Mardegian relieved Cmdr. Douglas R. Sattler, Jr., as comnmanding officer of the San Juan.

July 18, The San Juan made a brief stop off the coast of Groton for personnel transfer; Brief stop off Groton again on July 21; Moored at Pier 8S on July 29; Underway again on Aug. 16; Brief stop off Groton on Aug. 22; Moored at Pier 6S on Sept. 2; Underway again on Oct. 11; Brief stop off Groton on Oct. 14 and 19th.

October 21, USS San Juan moored at Pier 8N on Naval Submarine Base New London; Underway again on Nov. 1; Moored at Pier 31S for a brief stop on Nov. 7; Brief stop off Groton on Nov. 11; Returned home on Nov. 21.

December 21, USS San Juan departed Groton for a scheduled deployment.

March 3, 2023 The San Juan moored at Berth 3, Pier 1 on Naval Station Rota, Spain, for a 13-day port call.