The body of the unidentified man fell into a garden in Clapham, south London at approxiately 3:41 pm on Sunday, according to the airline.
It is thought the man had been hiding in the undercarriage of the aircraft before his fall.
The owner of the garden called police, who linked the discovery to a Kenyan Airways flight from Nairobi to Heathrow.
In a statement issued on Monday, the airline said it was cooperating with both British and Kenyan authorities in their investigations.
On inspection of the plane after landing, Heathrow police found a bag containing food and some clothing at the rear left landing gear.
A statement from Scotland Yard said: “A post-mortem examination will be carried out in due course.
“Police are working to establish the man’s identity.”
The 4,250-mile flight from Nairobi’s Jomo Kenyatta International Airport to Heathrow Airport takes approximately eight hours and 50 minutes.
This is not the first incident of a stowaway falling from a plane in London just before landing.
In 2012, a Mozambican man died after falling from the undercarriage of a Heathrow-bound flight from Angola.