Screening will start at Terminal 1 among passengers flying into the UK from countries at risk, before being extended to other terminals, Gatwick airport and Eurostar by the end of the week.
Passengers will have their temperatures taken, complete a risk questionnaire and have contact details recorded. Anyone with suspected Ebola will be taken to hospital.
Despite this, only a "handful" of cases - thought to be fewer than 10 - are expected to reach the UK before Christmas.
Last month, around 1,000 people arrived in the UK from Ebola-affected countries in West Africa. Officials say that people flying from Liberia, Sierra Leone and Guinea - where Ebola has killed more than 4,000 people - will be identified by Border Force officers.
Also, 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.
The actual screening will be done by nurses and consultants from Public Health England.
However, a spokesman for Heathrow stressed that the "government assesses the risk of a traveller 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.
However health experts questioned whether the enhanced screening would prevent the disease.
Dr Ron Behrens, from the London School of Hygiene and Tropical Medicine, told the Telegraph that the benefit of airport screening would be "very small", while there would be disruption to "large numbers of people".
"It appears not to be a scientific decision but a political one," he said.
