Gatwick Airport returned to normal on Sunday after computer problems led to delays on Saturday.
A BAA spokeswoman said paperwork had to be done by hand
Computer teams shut down the check-in system completely overnight to fix the problem by Sunday morning.
Problems began at the West Sussex airport on Friday evening with queues building up on Saturday after a manual check-in system was put in place.
On Sunday, the airport said the system was fixed overnight and the check-in system was running smoothly.
When the computer problem arose on Friday evening, all of the check-in areas in the south and north terminals, apart from the British Airways desks, were affected.
On Saturday evening, two check-in zones in the south terminal and some areas of the north terminal were still affected.
A spokeswoman said that IT specialists were working to put the problem right and the majority of the south terminal was back in action on Saturday.
She said: "We have brought in additional staff to help manage queues and are keeping people informed at the airport and the situation is gradually improving."
Passengers were advised to arrive "in good time".
Travel companies Thomas Cook, First Choice and Monarch Airlines said they had not experienced any problems, with flights leaving on time.
The airport said the main impact was that passengers were being slowed down as they went through check-in, but with minimum delay to flights.
Queues formed after paperwork including boarding passes had to be done by hand.
The BAA spokeswoman said: "We recognise that many people would have been affected and we want to apologise and reassure passengers that we are working very hard to rectify the situation."