Khan, 39, died on Tuesday at Kailahun hospital, in eastern Sierra Leone, an official statement said.
The virologist, who headed the Ebola center in Kenema, 300 kilometers (some 187 miles) east of the capital, Freetown, was regarded as a national hero after treating more than 100 people with the disease.
His death followed that of a colleague in Liberia on July 27, bringing to two the number of doctors killed by Ebola in that country.
Liberia has also lost about 15 health workers and one of its most important doctors, Samuel Brisbane, who worked at the John F. Kennedy hospital in Monrovia where Ebola patients were treated and isolated.
The Ebola epidemic in Guinea, Sierra Leone and Liberia has infected 1,201 people and killed 672 since the first case was reported in Guinea on March 22, according to the World Health Organization.
All the efforts of these countries to control the disease, for which there is no vaccine, have failed so far and the virus has continued to spread.
Last Thursday, Nigeria, Africa’s most populated country, registered it first victim, a man who had traveled to Liberia and died a few days after his return.
Nigeria has suspended operations of the ASKY airline in which the victim traveled, and its main air carrier, Arik Air, has cancelled all flights to Liberia and Sierra Leone.
Ebola causes serious hemorrhage and has a mortality rate of about 90 percent.
The disease is transmitted by direct contact with infected blood or body fluids, and is considered a threat to world health amid fears it might be used as a biological weapon.