Returning to Norfolk on 30 January, Robert E. Lee entered the Newport News drydock on 3 February for a month of shipyard work.

[citation needed] On 10 September 1963, Robert E. Lee entered the floating drydock Los Alamos (AFDB-7), then on 4 October 1963 resumed her normal patrol schedule.

Continuing to operate out of Holy Loch into 1964, she got underway on 27 November 1964 for her 16th patrol, which terminated on 28 January 1965 at Mare Island Naval Shipyard, Vallejo, California.

[citation needed] On 22 February 1965, Robert E. Lee entered the Mare Island Division of the San Francisco Bay Naval Shipyard for her first overhaul.

[citation needed] During the remainder of September and the first week of October, Robert E. Lee conducted shakedown operations off Cape Canaveral, Florida.

She returned to Charleston to commence a predeployment upkeep period at the Cooper River site in South Carolina where a failed rudder ram bolt was replaced.

[citation needed] In mid-August 1972, Robert E. Lee transited the Panama Canal and arrived in Charleston, South Carolina, on 14 September 1972.

[citation needed] In early 1977, Robert E. Lee drydocked for her third and final overhaul at Mare Island Naval Shipyard for nuclear reactor core refueling, equipment, and weapons upgrades.

Her hulk was stored at Puget Sound Naval Shipyard until it entered the Nuclear Powered Ship and Submarine Recycling Program.