Ten fire engines and about 70 firefighters were called to the London Oratory School on Seagrave Road in Fulham at 10am.
The fire is now under control and no injuries have been reported, the London Fire Brigade said.
The Met said the teenager was arrested at around 11.15am and remains in custody.
Part of an atrium in the four-storey building was damaged by fire.
The London Ambulance Service said it had not treated any patients.
A nearby shopping centre and some residential addresses have been evacuated as a precaution.
Residents were urged to keep their windows closed.
The prestigious Catholic school, which admits boys aged seven to 18 and girls aged 16 to 18, is a short distance from the Chelsea stadium, Stamford Bridge.
The school’s alumni include actor Simon Callow, trade unionist Mick Whelan as well as the children of the former prime minister Sir Tony Blair, Harriet Harman and former deputy prime minister, Sir Nick Clegg.
A spokesperson for London Fire Brigade said: “The brigade was called at 10.11am and is still at the scene.
“Fire crews from Fulham, Chelsea, Kensington, Wandsworth, Hammersmith, Clapham, Lambeth and Soho fire stations were in attendance.
“The cause of the fire is under joint investigation by the Brigade and the Met Police.”
A Metropolitan Police spokesperson said: “Police don’t know at this stage whether there are any injured persons inside the school.
“The cause of the fire is currently unknown and will be investigated.
“A nearby shopping centre and some residential addresses have been evacuated as a precaution.
“Road closures are in place. Please avoid the area at this time.”
The London Ambulance Service, which was on the scene, urged residents to close their windows.
A spokesperson said: “We sent a number of resources to the scene, including ambulance crews, an incident response officer, a medic in a fast response car and members of our hazardous area response team (HART).
“Our first medics arrived at the scene in less than three minutes.
“We did not treat any patients at the scene.”
Chelsea and Fulham MP Greg Hands said he was “concerned” by the incident, and was in touch with the police.
Posting on X, he added: “Lots of helicopter noise overhead this part of Fulham too.”