It posted a full-year loss of $723 million, too, almost wiping out its $840 million profit from 2011.
The fourth-quarter loss worked out to $1.87 per share. Excluding special items the loss would have been 58 cents per share, matching expectations of analysts surveyed by FactSet.
Superstorm Sandy cut $85 million from its results in 2012's final quarter.
A year ago the company lost $138 million, or 42 cents per share.
United's switch to a single passenger-information system last year caused problems with its website and frustrated some of its most lucrative customers when they couldn't get upgrades to first-class seats. Some of its customer service workers at airports struggled with new software on their computers, creating long lines.
Those problems drove potential customers away. Traffic fell 3.2 per cent in the fourth quarter. United reduced the amount of flying it did, too, so its planes were actually slightly fuller.
The company is aiming to put those issues behind it. It has said the technology issues are solved.
"With much of our integration behind us, our significantly improved operational performance and our increasing customer satisfaction, we can now go forward as one company," said Jeff Smisek, chairman, president, and CEO of United Continental Holdings Inc.
Revenue for the full year ticked up slightly to $37.15 billion.
"We see improvement this year and expect UAL to narrow the gap between itself and peers on revenue performance," S&P Capital IQ analyst Jim Corridore wrote in a note.
But he added that the company's "ongoing integration challenges keep us cautious on the shares, despite our positive view on the overall U.S. airline industry."
Shares of the Chicago-based United Continental Holdings Inc. rose 50 cents, or 2 per cent, to $25.50 in midday trading after rising to a 52-week high of $26.37 in earlier.