"Stonewall Jackson" departed Vallejo on 3 September 1964 for her shakedown cruise to Cape Kennedy, Florida. The Blue Crew completed training with a successful Polaris ballistic missile firing on 2 December 1964 and was relieved by the Gold Crew. Following the Gold Crew's successful Polaris missile launch on 16 December 1964, "Stonewall Jackson" returned to the Pacific Ocean to complete shakedown operations. She began post-shakedown alterations and repairs on 13 February 1965, then made final preparations at Bangor, Washington for an overseas deployment. In April 1965, she began her first strategic deterrent patrol.