The man was diagnosed with the rare tropical disease after flying into Glasgow on Tuesday. He was returning from Kabul in Afghanistan.
He was  transferred on Friday to the Royal Free Hospital in London on a special RAF isolation aircraft.
A spokesman for the hospital confirmed on Saturday morning that the man had died.
The Royal Free Hospital houses the national specialist centre for the management of patients with hazardous infections.
It is the first case of CCVHF to have been confirmed in the UK.
The patient had originally been admitted to the specialist Brownlee unit in Glasgow's Gartnavel General Hospital less than three hours after returning to the city on Emirates flight EK027 from Dubai.
He had driven home from Glasgow Airport using his own vehicle before seeking medical help.
Two passengers sitting close to him on the flight from Dubai are being monitored as a precaution.
But a further two passengers who were also contacted by health authorities do not require any follow-up, Greater Glasgow and Clyde health board has said.
Public health consultant, Dr Syed Ahmed, who is coordinating the investigations into this case, said: "The risk of person to person transmission of Crimean Congo Viral Haemorrhagic Fever is very low as it can only be transmitted by direct contact with infected blood and body fluids.
"It is not a virus which is transmitted through the air.
"The monitoring of these two passengers is purely precautionary and is in line the national guidance for the management of cases such as this."
The health authority has said the risk to all other passengers was "extremely low" but advised anyone with concerns to contact NHS 24.
CCVHF is a zoonosis - a disease found in animals that can infect humans.
Outbreaks are usually linked to contact with blood or body fluids from infected animals or people.
Onset is sudden, with initial symptoms including high fever, joint pain, stomach pain, and vomiting.
Red eyes, a flushed face and red spots in the throat are also common.
As the illness progresses, patients can develop large areas of severe bruising, severe nosebleeds, and uncontrolled bleeding.
A 38-year-old man who contracted Crimean-Congo Viral Haemorrhagic Fever (CCVHF) has died in hospital.