Khan became infected last week and had been in quarantine in an Ebola ward run by Medecins Sans Frontiere.
His death was confirmed by chief medical officer Dr. Brima Kargbo, who said his passing "is a big and irreparable loss to Sierra Leone as he was the only specialist the country had in viral hemorrhagic fevers."
Medical workers are especially at risk of contracting the deadly virus. After his infection was made public, Sierra Leone's Awareness Times reported health workers at the Kenema Ebola Center "allege Ministry of Health & Sanitation is 'incapable' of protecting the staff."
Kargbo has previously said that more help is needed. "We have a limited capacity and our health workers are not well prepared," telling the World Health Organization, "The external assistance is very much appreciated."
Sierra Leone is among three West African nations most affected by the Ebola outbreak. Guinea and Liberia are also grappling with the deadly virus. Earlier this month, WHO established a coordination center in Guinea's capital, Conakry, to assist with resource mobilization to the infected areas.
As of July 27, WHO reported a total of 672 deaths and 1,201 cases from confirmed, probable and suspected Ebola in Guinea, Liberia and Sierra Leone.
The Ebola virus is spread by close contact and kills up to 90 percent of its victims. There is no known cure or antivirus.