In 2000, the squadron dropped several bombs on selected tactical targets in southern Iraq, and continued to patrol the skies in the Persian Gulf.

In July 2002, the squadron left NAS Lemoore for a regularly scheduled six-month deployment aboard Abraham Lincoln, seeing action over Afghanistan as part of Operation Enduring Freedom as well as over Iraq, in support of Operation Southern Watch.
In late 2002, as the United States moved closer to military action against Iraq, Abraham Lincoln was ordered to stay on station in the Persian Gulf.
After a total of three extensions and approaching the ship's tenth month away from home, the Iraq War began.

On 19 March 2003, the squadron began combat sorties, participating in the first-night air strikes on Baghdad.
The squadron sustained an average of 20 daily combat sorties, while striking targets in Basra, An Nasiriya, Al Kut, Najaf, Al Hillah and ultimately Baghdad.
The squadron’s 272 combat sorties over 18 straight days struck the Iraqi regime’s Medina, Baghdad, and Nebuchadnezzar Armored Divisions, military airfields, facilities and command and control infrastructure.
VFA-25 returned to the United States in May 2003.

VFA-25 deployed aboard USS John C. Stennis in May 2004 to the Western Pacific, returning 1 November 2004.

From January to July 6, 2006, VFA-25 deployed with CVW-14 in support of the Iraq War and Valiant Shield aboard USS Ronald Reagan on her maiden voyage.
In January 2007, VFA-25 deployed for a 3-month "surge deployment" to the U.S. Seventh Fleet Area of Operations.
VFA-25 deployed again to the WESTPAC from June to November 2008.

On May 28, 2009, VFA-25 and Carrier Air Wing 14 deployed with USS Ronald Reagan on a deployment to the 7th and 5th Fleet Areas of Responsibility.

In 2010, VFA-25 joined Carrier Air Wing Seventeen deployed aboard USS Carl Vinson sporting the "AA" tailcode leaving Carrier Air Wing Fourteen and the "NK" tailcode for the first time in decades.

Following a successful combat deployment in support of Operation Enduring Freedom in 2012, VFA-25 returned to NAS Lemoore to transition to the F/A-18E Super Hornet, completing the transition in late January 2013 and was reassigned to CVW-9.

In 2019, the Squadron deployed aboard USS Abraham Lincoln as part of Carrier Air Wing 7 for the ship's homeport change to San Diego.
In 2000, the squadron dropped several bombs on selected tactical targets in southern Iraq, and continued to patrol the skies in the Persian Gulf.
In July 2002, the squadron left NAS Lemoore for a regularly scheduled six-month deployment aboard Abraham Lincoln, seeing action over Afghanistan as part of Operation Enduring Freedom as well as over Iraq, in support of Operation Southern Watch. In late 2002, as the United States moved closer to military action against Iraq, Abraham Lincoln was ordered to stay on station in the Persian Gulf. After a total of three extensions and approaching the ship's tenth month away from home, the Iraq War began.
On 19 March 2003, the squadron began combat sorties, participating in the first-night air strikes on Baghdad. The squadron sustained an average of 20 daily combat sorties, while striking targets in Basra, An Nasiriya, Al Kut, Najaf, Al Hillah and ultimately Baghdad. The squadron’s 272 combat sorties over 18 straight days struck the Iraqi regime’s Medina, Baghdad, and Nebuchadnezzar Armored Divisions, military airfields, facilities and command and control infrastructure. VFA-25 returned to the United States in May 2003.
VFA-25 deployed aboard USS John C. Stennis in May 2004 to the Western Pacific, returning 1 November 2004.
From January to July 6, 2006, VFA-25 deployed with CVW-14 in support of the Iraq War and Valiant Shield aboard USS Ronald Reagan on her maiden voyage. In January 2007, VFA-25 deployed for a 3-month "surge deployment" to the U.S. Seventh Fleet Area of Operations. VFA-25 deployed again to the WESTPAC from June to November 2008.
On May 28, 2009, VFA-25 and Carrier Air Wing 14 deployed with USS Ronald Reagan on a deployment to the 7th and 5th Fleet Areas of Responsibility.
In 2010, VFA-25 joined Carrier Air Wing Seventeen deployed aboard USS Carl Vinson sporting the "AA" tailcode leaving Carrier Air Wing Fourteen and the "NK" tailcode for the first time in decades.
Following a successful combat deployment in support of Operation Enduring Freedom in 2012, VFA-25 returned to NAS Lemoore to transition to the F/A-18E Super Hornet, completing the transition in late January 2013 and was reassigned to CVW-9.
In 2019, the Squadron deployed aboard USS Abraham Lincoln as part of Carrier Air Wing 7 for the ship's homeport change to San Diego.
VFA-25