A “handful” of cases – thought to be fewer than 10 – are expected to reach the UK before Christmas.
Screening will start at Terminal 1, before being extended to other terminals, Gatwick airport and Eurostar by the end of the week.
In September, around 1,000 people arrived in the UK from Ebola-affected countries in West Africa.
People flying from Liberia, Sierra Leone and Guinea will be identified by Border Force officers.
Nurses and consultants from Public Health England will then carry out the actual screening.
Passengers will have their temperatures taken, complete a risk questionnaire and have contact details recorded.
Anyone with suspected Ebola will be taken to hospital.
Passengers deemed to be at high risk due to contact with Ebola patients, but who are displaying no symptoms, will be contacted daily by Public Health England.
Ebola has killed more than 4,000 people in Liberia, Sierra Leone and Guinea.
A spokesman for Heathrow said the welfare of “our passengers and colleagues is always our main priority”.
He added: “We would like to reassure passengers that the government assesses the risk of a traveler contracting Ebola to be low.”
There is no direct flight to the UK from Liberia, Sierra Leone or Guinea so people could arrive at airports that do not screen passengers.
Instead “highly visible information” will be in place at all entry points to the UK.
The Department of Health estimates that 85% of all arrivals to the UK from affected countries will come through Heathrow.
However, screening arrivals marks a rapid shift in policy from the UK government.
Just last week, it said there were no plans for screening as people were tested before leaving affected countries.
The WHO said it was unnecessary and that it would mean screening “huge numbers of low-risk people”.
Anyone in the UK with suspected Ebola will be taken to hospital and blood samples will be taken to Public Health England’s specialist laboratory for rapid testing.
If the test is positive, then the patient will be transferred to an isolation unit at the Royal Free Hospital in London. It is the centre that cared for the British nurse William Pooley, who contracted Ebola in West Africa.
Hospitals in Newcastle, Liverpool and Sheffield are on standby to offer similar facilities if there is a sudden surge in Ebola cases. A total of 26 isolation beds could be prepared at the four hospitals.
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