The drone sighting came just as the hub was trying to get operations back to normal after a more than 24-hour suspension that disrupted travel for more than 120,000 people.
At least 25 flights were cancelled with others severely delayed while trackers suggested planes were being diverted to Stansted, Luton and Heathrow after the last plane landed at Gatwick at 4.59pm.
Just over an hour later Gatwick said planes had returned to the air, saying the 'military measures in place at the airport' would ensure the safety of passengers.
The Army had earlier used jamming devices in the hope of knocking the drone out of the sky as police scoured the Sussex countryside in a bit to find the culprit.
When Gatwick restarted earlier in the day, it offered no guarantees that the mystery devices were gone, though a variety of steps were taken to make the airport safe.
Sussex police, who have been dealing with the incident along with specialists from Britain's armed forces, had said that during the initial occurrences, almost 50 drone sightings were reported at the airport between 9.07pm on Wednesday and 4.25pm on Thursday, though some may have been duplicates. A statement on the force's website said that "as yet, the drone has not been identified".
The British Airline Pilots' Association said it's "extremely concerned" at the continuing risk of a drone collision and that craft could go unseen around Gatwick's perimeter or obstruct flight paths outside the detection zone.
The airport is Britain's second busiest and the biggest hub for EasyJetc, as well as being a focus for long-haul leisure flights a British Airways. It also counts Virgin Atlantic Airways, Norwegian Air Shuttle, Thomas Cook and TUI as major operators. Ryanair Holdings, which has a limited presence at Gatwick, switched Friday flights to its main Stansted base.
The hub has only one runway, which is already the world's busiest, offering little scope to cram in more flights even if the drones stay away.
UK authorities portrayed the intrusion as deliberate, with Gatwick Chief Executive Officer Stewart Wingate saying it had been "highly targeted" and designed to deliver maximum disruption in the days before Christmas. Police said the actions were clearly intentional, though most likely not terror related.
The pair of drones got the better of a multi-fronted operation for the best part of two days. A daylight search backed by helicopters failed to locate the devices or their operator, prompting the Ministry of Defence to send in army personnel equipped with specialist gear as night fell Thursday.
In a bid to ease the backlog of flights, the Department for Transport temporarily lifted a ban on night operations at other UK airports.
Unmanned aerial vehicles and laser pointers are becoming an increasing threat for aircraft, prompting regulators to come up with new rules against operating the devices near airfields.
Dubai International Airport shut down temporarily in 2016 after suspected drone activity, while airspace around Wellington, New Zealand, was closed for 30 minutes this year when a craft was spotted flying close to the runway. And Grupo Aeromexico SAB last week said was investigating whether a drone collided with a Boeing Co. 737 aircraft as the plane approached Tijuana, Mexico. The jet sustained damage to its nose but landed safely.
While governments bar drones from paths reserved for airliners, with Britain outlawing flights above 400 feet or within 1 kilometre of an airport boundary, the millions of small consumer devices that have been purchased around the world can't be tracked on radar.
That makes it difficult to enforce the rules. In addition, many users don't know the restrictions, or don't follow them, despite the threat of a five-year jail term for perpetrators in the UK.
Transport Secretary Chris Grayling told the BBC on Friday that a variety of anti-drone protection technologies have been deployed at Gatwick, while adding that authorities still have no idea who was behind the raids.
"We've had to assemble a variety of different measures around that airport to make sure it's safe," he said. "This is an unprecedented event. There's not been anything like this anywhere in the world."