Thousands of passengers are affected as airlines struggle to move aircraft and crew to their scheduled location after an issue at the West Sussex airport's control tower caused flights to be suspended for more than two hours on Wednesday night.
The problem was resolved but the knock-on effect is continuing to cause disruption, with six flights cancelled and a further 39 delayed between 6am and midday on Thursday, according to aviation data website FlightStats.
British Airways, easyJet and Norwegian were among the airlines affected by the closure of the runway.
On Wednesday, at least 26 flights were diverted and eight cancelled as the airport worked with ANS, its air traffic control provider, to fix the problem.
Gatwick issued an apology and urged passengers to check the status of their flight with their airline before going to the airport.
Travel journalist Shilpa Ganatra, who was supposed to be flying to Bilbao for a festival, learnt her flight was cancelled at the airport on Wednesday night.
She said: "Vueling, who I was flying with, rebooked me on a Friday, indirect, overnight flight, which is obviously pointless.
"I'm just trying to find out how to reject that - I've had to rebook myself on a 6.30am Ryanair flight from Southend tomorrow, at a cost of £280 plus £60 in hotel and yet-to-find-out train fare.
"I'm hoping either my travel insurance or the airline will cover it, but it's the stress of not being 100% sure and the hassle that's the most infuriating thing, apart from the lost holiday time."
She said other travellers "had it worse", with people "waiting hours to find out what was going on".
Jennifer Jones, 31, from Hertfordshire, said her Norwegian Airlines flight which left Stockholm at 5.50pm on Wednesday was diverted to Birmingham Airport.
Passengers were sat on the tarmac for an hour-and-a-half while their plane waited in a queue to refuel and fly to Gatwick.
"Everyone is pretty relaxed but bored I think," she said.
"A few people have asked for food but they said they can't do a food service right now."
The airport was forced to shut its runway four times in two days in April 2018 after only one air traffic controller was available to work due to a staff shortage.
The runway was closed every time the person took their two mandatory breaks per shift.