AP Photo/Pablo Martinez Monsivais
Frontier said Wednesday that Dave Siegel stepped down for personal reasons.
Siegel's departure comes two days after the government said that Frontier had the highest complaint rate and the worst on-time performance among the nation's 14 leading airlines in March.
Frontier, based in Denver, said that Chairman Bill Franke will manage strategy and finances and President Barry Biffle will handle daily operations. Siegel had led Frontier since January 2012.
Privately held Frontier has been shifting to a so-called ultra-low-cost carrier that offers low base fares but adds fees for many services.
Customer complaints have soared. In March, passengers were 34 times more likely to complain about Frontier than about Southwest Airlines, according to the U.S. Department of
More than one-third of Frontier's March flights arrived at least 15 minutes late.
Frontier operates a hub at Denver International Airport and flies throughout the U.S. and to Mexico, Costa Rica and the Caribbean.
Republic Airways sold Frontier to investment firm Indigo Partners in 2013. Franke is Indigo's managing partner.