Carl Vinson departed on her fifth deployment (again with CVW-15) on 1 February 1990, the last deployment for the A-7 Corsair.
The ship returned to Alameda on 30 July 1990.
On 22 September 1990, Carl Vinson entered the yards at Bremerton Naval Station, Washington for a 28-month complex overhaul (COH).
The carrier received her first COMNAVAIRPAC Battle "E" award for 1990.

On 17 February 1994, the carrier, with Carrier Air Wing Fourteen embarked, departed for the Persian Gulf in support of Operation Southern Watch.
The carrier returned to Alameda on 17 August 1994, receiving her third Admiral Flatley Award for aviation safety.

In 1995, a documentary entitled Carrier: Fortress at Sea was aired on the Discovery Channel, which chronicled the carrier's six-month-long voyage to and from the Persian Gulf.

From 26 August until 3 September 1995, Carl Vinson participated in Exercise Ke Koa, as well as ceremonies to commemorate the end of World War II in the Pacific.
During these ceremonies, President Bill Clinton visited the ship in Hawaii.
As part of the commemoration ceremonies, Carl Vinson launched 11 World War II-era planes.

The ship departed for her seventh deployment 14 May 1996, heading for the Persian Gulf with CVW-14 in support for Operation Southern Watch and Operation Desert Strike.
The ship also participated in Exercise Rugged Nautilus before returning to Alameda on 14 November 1996.

With the closing of Naval Air Station Alameda, the ship was transferred to Bremerton, Washington, arriving at her new homeport on 17 January 1997, where she played host to the last carrier launch and recovery operations for the A-6E Intruder.

In 1998 with Carrier Air Wing Eleven (CVW-11) embarked, the ship participated in RIMPAC '98.
During the exercise on the morning of 10 August, the Australian diesel-electric submarine HMAS Onslow located the 'enemy' carrier and 'sank' her.
Onslow closed to within 300 meters (980 ft) without being detected, then released green flares to indicate her location, 'sinking' the supercarrier.
Carl Vinson then departed for the Persian Gulf, launching airstrikes on 19 December 1998 in support of Operation Desert Fox and Operation Southern Watch.
These strikes continued into March 1999.
In July 1999, Carl Vinson was drydocked in the Puget Sound Naval Shipyard for 13 months as the Navy spent more than $230 million to upgrade the ship.
Post refit shakedowns continued into 2000.
Carl Vinson departed on her fifth deployment (again with CVW-15) on 1 February 1990, the last deployment for the A-7 Corsair. The ship returned to Alameda on 30 July 1990. On 22 September 1990, Carl Vinson entered the yards at Bremerton Naval Station, Washington for a 28-month complex overhaul (COH). The carrier received her first COMNAVAIRPAC Battle "E" award for 1990.
On 17 February 1994, the carrier, with Carrier Air Wing Fourteen embarked, departed for the Persian Gulf in support of Operation Southern Watch. The carrier returned to Alameda on 17 August 1994, receiving her third Admiral Flatley Award for aviation safety.
In 1995, a documentary entitled Carrier: Fortress at Sea was aired on the Discovery Channel, which chronicled the carrier's six-month-long voyage to and from the Persian Gulf.
From 26 August until 3 September 1995, Carl Vinson participated in Exercise Ke Koa, as well as ceremonies to commemorate the end of World War II in the Pacific. During these ceremonies, President Bill Clinton visited the ship in Hawaii. As part of the commemoration ceremonies, Carl Vinson launched 11 World War II-era planes.
The ship departed for her seventh deployment 14 May 1996, heading for the Persian Gulf with CVW-14 in support for Operation Southern Watch and Operation Desert Strike. The ship also participated in Exercise Rugged Nautilus before returning to Alameda on 14 November 1996.
With the closing of Naval Air Station Alameda, the ship was transferred to Bremerton, Washington, arriving at her new homeport on 17 January 1997, where she played host to the last carrier launch and recovery operations for the A-6E Intruder.
In 1998 with Carrier Air Wing Eleven (CVW-11) embarked, the ship participated in RIMPAC '98. During the exercise on the morning of 10 August, the Australian diesel-electric submarine HMAS Onslow located the 'enemy' carrier and 'sank' her. Onslow closed to within 300 meters (980 ft) without being detected, then released green flares to indicate her location, 'sinking' the supercarrier. Carl Vinson then departed for the Persian Gulf, launching airstrikes on 19 December 1998 in support of Operation Desert Fox and Operation Southern Watch. These strikes continued into March 1999. In July 1999, Carl Vinson was drydocked in the Puget Sound Naval Shipyard for 13 months as the Navy spent more than $230 million to upgrade the ship. Post refit shakedowns continued into 2000.
USS Carl Vinson