Early on Saturday, Gatwick said flights would be operating but warned of further disruption.
“Our runway is open and we aim to run a full schedule on Saturday,” it said on the website.
“Passengers should expect some delays and cancellations as we continue to recover our operations following three days of disruption and are advised to check with their airline before travelling to the airport.”
A Gatwick spokesman said around 1,000 aircraft have been cancelled or diverted, affecting approximately 140,000 passengers, since Wednesday night.
The knock on effect of cancellations and delays was continuing to have an impact on Virgin Atlantic flights.
Its first flight of the day, to St Lucia and Tobago, took off an hour late, and three more flights were delayed soon after.
The 13:00 flight to Orlando has been delayed by two hours and the 12:15 to Cancun, Mexico is one hour behind schedule.
At the check in desks, children were being distracted by free candy canes handed out by staff.
Neil Martin, 48, from Ukfield, Sussex, who was travelling to Cancun with his wife and three daughters, was among those delayed.
He said: “An hour delay after everything that’s happened is completely acceptable. I’m just glad we are going. Everyone has been really helpful so far and we’re looking forward to getting away.”
EasyJet’s first 39 flights on Saturday all suffered delays, some by as much as nearly five hours.
Norwegian have had six of their 25 flights delayed.
The worst queues were in Gatwick’s south terminal, where Thomas Cook saw all eight of their flights delayed on Saturday morning.
Lines of people continued to snake through the terminal and out into the train station ticket concourse.
Tom Hawkins and his family arrived early for their flight to Fuerteventura.
“We anticipated disruption so made sure to get here in good time,” he said.
Drone ‘buzzed’ the tower
In a move known as “buzzing the tower”, it emerged the perpetrator had taunted airport staff by circling the drone around the building and flashing its lights, an industry source told The Telegraph.
A detailed description of the drone, provided by witnesses, meant experts were able to determine the make and model of the machine, which is only available from a handful of locations in the UK.
The heightened level of panic around the airport was demonstrated on Friday evening when all flights had to be temporarily suspended after a drone was reportedly spotted in the air.