It is the first time the MoD has confirmed a civilian casualty during the UK’s campaign against the terror group in Iraq and Syria.
Defence Secretary Gavin Williamson described the “unintentional civilian fatality” on 26 March as “deeply regrettable”.
The RAF had targeted three IS fighters in eastern Syria when a civilian motorbike “crossed into the strike area at the last moment”, he said.
“These events serve to remind us of the consequences of conflict and of the heavy price that the people of Syria have paid.
“It reminds us that when we undertake military action, we must do so knowing that it can never be completely without risk.
“Such incidents will not weaken our resolve to defeat Daesh (IS) and rid the world of its poisonous ideology of hate and intolerance.”
The MoD said an RAF Reaper drone had tracked a group of terrorists in a vehicle in the Syrian Euphrates valley and “successfully destroyed it and its occupants with a precision Hellfire missile attack”.
It concluded that a civilian had been killed following “detailed post-strike analysis” of the airstrike, Mr Williamson said.
The RAF has conducted more than 1,600 airstrikes in Iraq and Syria – second only to the US – and many of them have been in dense urban areas.
Sky’s defence correspondent Alistair Bunkall said: “The military has been heavily criticised in the past for refusing to concede its airstrikes might have caused civilian deaths, especially because the United States is more ready to acknowledge such incidents.
“Some figures put civilian casualties in Iraq and Syria at more than 5,000, although official figures are much lower.”
Previously, the UK’s most senior general in Iraq has spoken out about the realities of war, saying civilian deaths are “the price you have to pay” for defeating extremists.
Major-General Rupert Jones said that the coalition goes to the “greatest possible lengths” to avoid civilian casualties, but said that war is “hell”.
Last month, Theresa May ordered British armed forces to join the US and France in conducting “co-ordinated and targeted” airstrikes on the Syrian regime’s chemical weapons facilities.
French president Emmanuel Macron had said the military action on 7 April ended “without any human life loss”.