With MLB's reorganization of the minor leagues after the 2020 season, Lancaster was not selected to continue in affiliated baseball, and ultimately folded.

They made the move to Lancaster in 1996. Notable players to play for the JetHawks include José Cruz Jr. and Brandon Webb.

In November 2005, the original owners of the JetHawks during their first 10 years in Lancaster, Clutch Play Baseball, LLC, sold the team to a group led by majority investor Peter Carfagna of Cleveland, Ohio.

Since the Fenway Sports Group purchased the Carolina League's Salem Avalanche franchise after the 2007 season, with the stated intent of moving the Red Sox's High-A affiliation there once the 2007–2008 agreement term expired, the JetHawks were forced to find a new major league affiliate before the 2009 season—the Houston Astros.

Wes Clemente, after serving the 2009 season as the JetHawks' manager, took over the managerial position for the Corpus Christi Hooks, Houston's Double-A affiliate.

On May 26, 2011, the Lancaster JetHawks announced that Larry Thornhill had resigned his position as vice president and general manager of the franchise for personal reasons.

Seymour currently also serves as vice president and general manager of the Lake County (OH) Captains, Class A affiliate of the Cleveland Indians under the direction of the Peter A. Carfagna ownership group which also controls the Lancaster JetHawks.

In the Southern Division Championship Series, the JetHawks beat the First & Second Half Champion High Desert Mavericks, three games to one.

On May 12, 2013 (Mother's Day), the Lancaster JetHawks beat the Stockton Ports, 2–0, as Kyle Hallock and Luis Cruz combined to throw the first nine-inning no-hitter in franchise history.

On April 29, 2014, Lance McCullers Jr. and Kyle Smith combined to tie a Lancaster franchise record with 17 strikeouts against the High Desert Mavericks.

The record was set on August 8, 1997, when then Mariners' farmhand Jason Bond struck out 14 batters and the bullpen fanned three at Recreation Park against the Visalia Oaks.

On May 13, 2014, Josh Hader, J. D. Osborne, and Daniel Minor combined to throw the third no-hitter in franchise history as the JetHawks beat the Bakersfield Blaze, 1–0, at the Hangar.

On June 5, 2014, designated hitter Dan Gulbransen doubled to lead of the eighth inning to complete the sixth cycle of JetHawks history in a 16–7 win over the Inland Empire 66ers at the Hangar.

On June 11, 2014, the Lancaster JetHawks clinched the 2014 South Division First Half Championship title with a 16–3 win over the Rancho Cucamonga Quakes at the Hangar.

As manager of the Class A Quad Cities River Bandits in 2013, Lopez led the club to the Midwest League Championship title after an 81-57 finish in the regular season.

In the Southern Division Championship Series, the JetHawks lost to the First Half Champion High Desert Mavericks, three games to one.

After winning the first half title for the 2017 season, the JetHawks sent a record nine players to participate in the California League All-Star Game at Recreation Ballpark in Visalia on June 20.

The JetHawks' all-star position player reserves include catcher Hamlet Marte and infielder/outfielder Mylz Jones.

In the Southern Division Championship Series, the JetHawks beat the wild card Rancho Cucamonga Quakes, three games to one.

In the California League Championship Series, the JetHawks lost to the North Division Champion Modesto Nuts, three games to none.

Lancaster's all-stars included right-handed pitchers Rico Garcia, Heath Holder, Reid Humphreys, and Justin Lawrence along with infielders Roberto Ramos, Alan Trejo, and Colton Welker as well as outfielder Vince Fernandez.

It included many aspects of the original organization, such as new merchandise, new uniforms, and caps for the players to wear during games along with "El Viento" themed giveaways.

For each "El Viento" night, The Hangar had taco trucks, free activities for kids, and music as part of Minor League Baseball's "Copa de la Diversión" (Spanish for "Fun Cup") in an effort to honor and embrace U.S. Hispanic and Latino culture.

[3] The city and team explored options to continue play in 2021, including a potential arrangement with the Pecos League.

"The entire Lancaster community has embraced the city's mission to become the alternative energy capital of the world, and as the first minor league team in California to go solar, we’re happy to do our part", said JetHawks owner Peter Carfagna.

The free service launched on Saturday, September 5, 2009, at 6 pm with an hour-long pre-game show leading up to dual coverage of the Lancaster JetHawks game against the Inland Empire 66ers of San Bernardino and the Antelope Valley College Marauders football opener on the road against College of the Canyons.

The team partnered with News Talk 1380, a High Desert Broadcasting station, which will carry every JetHawks game, including the regular season and playoffs.

Jeff Lasky, JetHawks' play-by-play broadcaster since the 2006 season, will once again be calling the action while being joined by newcomer Scott Blusiewicz.

Before the 2009 season on March 21, 2009, KaBoom celebrated his 13th birthday at a party held in his honor at Clear Channel Stadium, where he revealed his younger brother, Stealth, to JetHawks fans.