She served on patrol duties between 1964 and 1966 during the Indonesian Confrontation. On 3 June 1964, Parramatta and sister ship Yarra met the troop transport HMAS Sydney off the Philippines and escorted her to Kota Kinabalu, Singapore, and Penang to deliver Australian military units and supplies. Parramatta then escorted the former aircraft carrier back to Fremantle: the return voyage to Australia was interrupted on the morning of 23 June by the detection of a suspected Indonesian submarine: the two Australian ships performed evasion tactics for eighteen hours before resuming the voyage. Other deployments were made during 1965 and 1966, with this service later recognised by the battle honour "Malaysia 1964–66"
Parramatta also had active service during the Vietnam War, escorting the fast troop transport HMAS Sydney (III) to Vung Tau, Vietnam. During late May and early June 1965, Parramatta was one of several ships escorting Sydney on her first troop transport voyage to Vietnam. Parramatta and Sydney also worked together on the latter's tenth Vietnam voyage during March and April 1968. Parramatta's third escort run with Sydney occurred in May 1971; the former carrier's twentieth Vietnam voyage.
In July 1976 Parramatta was diverted to the Indonesian island of Bali to provide humanitarian relief following an earthquake which killed over 500 Balinese and injured another 3,000.
Highlights of her second commission included a rare visit to the Peoples Republic of China in 1986 and participation in 1986 Royal Australian Navy 75th Anniversary Naval Review and the Bicentennial Naval Salute in 1988.
Parramatta was decommissioned on 11 January 1991 as the River Class Destroyer Escorts were replaced by the Adelaide Class Guided Missile Frigates. She was sold to a Pakistani company and towed from Australia October 1991 to be broken up.
The ship's twin 4.5 inch Mark 6 gun turret, along with the captain's cabin from time of the ship's decommissioning, are preserved at the RAN Naval Heritage Collection Repository on Spectacle Island, Sydney