The new aircraft, known as 13 Squadron, which were officially "stood up" in October, started flying missions over Afghanistan this week from their base in Lincolnshire.
The hi-tech Reaper drones are primarily used to gather intelligence on enemy activity on the ground, but they also carry 500lb bombs and Hellfire missiles for precision strikes on insurgents.
An MoD spokesman said they had been carrying out missions including intelligence, surveillance and reconnaissance, but would not comment on exactly what individual missions had been flown in the past week by drones piloted from the UK.
War protester: 'Now is the time to ban killer drones'
Ahead of a planned protest outside an RAF base today against the UK's use of armed drones in Afghanistan, War on Want senior campaigns officer Rafeef Ziadah said:
Drones, controlled far away from conflict zones, ease politicians' decisions to launch military strikes and order extrajudicial assassinations, without democratic oversight or accountability to the public.
"Now is the time to ban killer drones - before it is too late.
Drones have been flown for the first time from Lincolnshire
Drone missions over Afghanistan have been flown by RAF pilots operating on British soil for the first time.
Until this week, RAF crews who control armed drones in Afghanistan have been operating from the USA Creech Air Force Base in Nevada.
Last year the Ministry of Defence (MoD) announced that the UK was doubling the number of armed RAF drones in Afghanistan to 10 with the five new aircraft to be operated remotely from RAF Waddington in Lincolnshire.
Anti-war protesters are set to gather outside an RAF base today to voice their opposition to the UK's use of armed drones in Afghanistan.
Members of the Stop The War Coalition, CND, The Drone Campaign Network and War on Want will march from Lincoln to nearby RAF Waddington.
The RAF began remotely operating its Reaper unmanned aerial vehicles deployed to Afghanistan from the Lincolnshire airbase earlier this week.
In a statement, the RAF said it had started supporting the International Security Assistance Force and Afghan ground troops with "armed intelligence and surveillance missions" remotely piloted from RAF Waddington.
The aircraft were previously operated from a United States Air Force base in Nevada.