The soldiers were travelling between bases in the northern city of Mazar-e-Sharif when they came under fire, according to a spokesman.
"There will be a follow-up operation as to who was shooting at them," the spokesman said. "We are treating it as a hostile incident rather than friendly fire."
The city was a stronghold for opposition to the former Taliban regime before Northern Alliance forces finally captured it in November 2001, assisted by Allied airstrikes.
The MoD said the troops had been travelling from the Provincial Reconstruction Team base, which houses international military and civilian personnel assisting the Afghan government with developing democratic institutions and disarming militias.
They were on their way to a forward support base when they were attacked.
John Reid, the Secretary of State for Defence, said: "My thoughts and sympathies are with the family and friends of the soldier tragically killed today." The MoD spokesman added: "It is with deep regret that the Ministry of Defence announces that there was one British fatality, and five injuries, sustained in this incident. Next of kin are being informed and we shall release more details in due course."
Mazar-e-Sharif is the site of one of the country's holiest shrines, the Blue Mosque, believed to mark the tomb of the Fourth Caliph, Ali.Reuse content