From Saturday, anyone who owns a drone weighing more than 250g must fill out an online form and pay a £9 fee to continue using it.
The Civil Aviation Authority (CAA) said just 40,000 of the UK’s estimated 90,000 drone users have registered since the system opened earlier this month.
Anyone who flies a drone will also need to have passed an online theory test featuring 20 multiple choice questions.
Users who fail to register or sit the competency test could face fines of up to £1,000.
The new rules are being introduced as part of a crackdown on drone misuse.
Department store John Lewis stopped selling drones in May because of the chaos they are causing at airports.
Drone sightings at Gatwick in December last year caused around 1,000 flights to be cancelled or diverted over 36 hours, affecting more than 140,000 passengers in the run-up to Christmas.
A number of other airports have been forced to suspend flights for several hours due to drone activity this year, including Heathrow.
UK Airprox Board figures show there were 125 near-misses between drones and aircraft reported in 2018, up by more than a third from 93 the previous year.
In March, the drone no-fly zone around airports was extended from 1km (0.6 miles) to 5km (3.1 miles).
CAA assistant director of communications Jonathan Nicholson said: “UK drone laws are changing and it’s vital that drone users – whether they fly regularly or not – are aware of how the drone registration scheme will affect them.
“Registration becomes law from the 30th November. If you are caught flying a drone from then, and unable to present proof of registration, you could be hit with a £1,000 fine.
“The online registration system has been designed to be as intuitive and accessible as possible, meaning those that need to register online can do so easily by the deadline.”
Drone users must visit register-drones.caa.co.uk to sign up to the scheme.
It is hoped the registration system will help reunite people with their lost drones as they will be linked to a unique ID which must be displayed on devices.