The Super Hornet achieved initial operating capability (IOC) in September 2001 with the U.S. Navy's Strike Fighter Squadron 115 (VFA-115) at Naval Air Station Lemoore, California. VFA-115 was also the first unit to take their F/A-18 Super Hornets into combat. On 6 November 2002, two F/A-18Es conducted a "Response Option" strike in support of Operation Southern Watch on two surface-to-air missile launchers at Al Kut, Iraq and an air defense command and control bunker at Tallil air base. One of the pilots, Lieutenant John Turner, dropped 2,000 lb (910 kg) JDAM bombs from the Super Hornet for the first time during combat.
In support of Operation Iraqi Freedom (Iraq War), VFA-14, VFA-41 and VFA-115 flew close air support, strike, escort, SEAD and aerial refueling sorties. Two F/A-18Es from VFA-14 and two F/A-18Fs from VFA-41 were forward deployed to the Abraham Lincoln. The VFA-14 aircraft flew mostly as aerial refuelers and the VFA-41 fighters as Forward Air Controller (Airborne) or FAC(A)s. On 6 April 2005, VFA-154 and VFA-147 (the latter squadron then still operating F/A-18Cs) dropped two 500-pound (230 kg) laser-guided bombs on an enemy insurgent location east of Baghdad.
On 8 September 2006, VFA-211 F/A-18F Super Hornets expended GBU-12 and GBU-38 bombs against Taliban fighters and Taliban fortifications west and northwest of Kandahar. This was the first time the unit had participated in an active combat capacity using the Super Hornet.
During the 2006–2007 cruise with Dwight D. Eisenhower, VFA-103 and VFA-143 supported Operations Iraqi Freedom, Enduring Freedom and operations off the Somali coast. Alongside "Legacy Hornet" squadrons, VFA-131 and VFA-83, they dropped 140 precision guided weapons and performed nearly 70 strafing runs.
In 2007, Boeing proposed additional F/A-18E/Fs to the U.S. Navy in a multi-year contract. As of October 2008, Boeing had delivered 367 Super Hornets to the U.S. Navy. On 6 April 2009, Defense Secretary Gates announced that the Department of Defense intended to acquire 31 F/A-18s in FY2010. Congress requested the DoD study a further multi-year contract so that a projected fighter shortfall could be averted; in 2006, the Navy was 60 fighters below its validated aircraft requirement. The FY2010 budget bill authorized a multiyear purchase agreement for additional Super Hornets. A multi-year contract was finalized on 28 September 2010, reported as saving $600 million over individual yearly contracts, for 66 Super Hornets and 58 Growlers to mitigate a four-year delay in the F-35 program.
On 7 August 2014, U.S. defense officials announced they had authorizated to launch bombing missions upon Islamic State forces in northern Iraq. The decision to take direct action was made to protect U.S. personnel in the city of Irbil and to ensure the safety of transport aircraft making airdrops to Yazidi civilians. Early on 8 August 2014, two Super Hornets took off from the USS George H.W. Bush and dropped 500 lb laser-guided bombs on a "mobile artillery piece" the militants had been using to shell Kurdish forces defending the city. Later that day, four more aircraft struck a seven-vehicle convoy and a mortar position.