On 1 November 1958, Chicago was reclassified CG-11 and towed to San Francisco Naval Shipyard to begin a five-year conversion to a guided missile cruiser. Begun on 1 July 1959, the entire superstructure was removed and replaced with new aluminum compartments, modernized electronic systems, and an improved Naval Tactical Data System (NTDS) equipped combat information center. Representative of the new technological focus on guided missiles, Chicago was refitted with Tartar and Talos SAM stowage, loading, launching, and guidance systems. Triple torpedo tubes, two ASROC launchers, two 5 in/38 cal guns, and two antisubmarine helicopters rounded out the cruisers’ modifications.
Designed to provide long-range air, surface, and sub-surface defense for task forces, Chicago was recommissioned at the San Francisco Naval Shipyard on 2 May 1964, and was assigned to Cruiser-Destroyer Flotilla Nine, Pacific Fleet. Preliminary acceptance trials were conducted throughout the summer until 2 September, when Chicago officially joined the 1st Fleet as an active unit. Following sonar calibration and deperming in Puget Sound the cruiser arrived at her home port of San Diego, California to begin weapons systems qualifications. Examination and evaluation of the new missile systems were completed by 2 December, following successful trials at the Pacific Missile Range off southern California.