After shakedown training by both crews and a repair period, Thomas Jefferson was assigned to Submarine Squadron 14 in early October 1963.

Thomas Jefferson completed two patrols in 1973 before returning to the United States to hold midshipman training from 18 June to 31 August.

On 1 July 1974, Thomas Jefferson entered the Mare Island Naval Shipyard for overhaul, refueling, and conversion to the Polaris A-3 missile system.

While operating out of San Diego in 1976, with the Blue Crew aboard, the ship experienced a complete loss of electrical power and propulsion.

After successful ascent, the boat proceeded under its own power back to San Diego where an investigation resulted in better training for the ORSE Board Examiners.

The Gold Crew took over the ship on 4 April and conducted additional post-overhaul shakedown operations which included a missile firing at Cape Canaveral, a transit of the Panama Canal, and a missile loadout at Bangor, Washington, before resuming deterrent patrol operations with the Pacific Fleet on 8 August.

The ship was reclassified as an attack submarine and redesignated SSN-618 on 11 March 1981 and retained primarily for training, antisubmarine warfare exercises, and other secondary duties.