Dr Godfrey George, medical superintendent of Kambia Government Hospital in northern Sierra Leone, died overnight, according to Sierra Leone's government.
George's death, which was announced by Dr Brima Kargbo, Sierra Leone's chief medical officer, was a blow to efforts to keep desperately needed health care workers safe in a country ravaged by the deadly virus.
George had been driven to the capital, Freetown, after reporting that he was not feeling well.
Doctors and nurses have been particularly vulnerable to contracting Ebola, as the virus is spread through bodily fluids.