Virgin America has emerged as America's best airline for the fourth year in a row.
JetBlue came second, followed by Delta Air Lines, according to Department of Transportation data presented in the 2016 Airline Quality Rating report.
Although overall industry performance improved in three of the four categories tracked, customer complains rose by 38 per cent from 2014 to 2015.
"This is the worst complaints have been for 15 years, as a rate. The last time it got this high was in 2001," report co-author Dean Headley, a researcher at Wichita State University's business school, told CNN.
Six of the 13 US airlines evaluated - JetBlue, Delta, ExpressJet, SkyWest, Southwest and United - improved their overall scores, while six others declined.
Delta, Alaska and Southwest maintained their positions this year, but United and American fell three places. American is the largest airline in the world and United is the third-largest carrier in the US. Spirit Airlines is new to the rankings.
Hawaiian Airlines came first in terms of on-time performance, arriving on-time 88.4 per cent of the time in 2015. Spirit Airlines, ranked last overall, had the worst on-time performance at 69 per cent.
Spirit also had the highest complaint rate with 11.73 out of 100,000 passengers registering complaints, while Alaska Airlines had the lowest complaint rate, with just 0.5 per 100,000 complaining.
Virgin America had the best record for baggage handling, while Envoy Air had the worst.
Envoy also had the highest rate of involuntary denied boardings - when airlines overbook their flights. JetBlue had the fewest overbooked flights.
