They are providing only emergency cover during a 24-hour walkout which started at 0800 GMT, meaning that several thousand routine operations have had to be cancelled, along with appointments and tests.
There are more than 55,000 junior doctors in Britain, making up a third of the medical workforce.
They are qualified medical practitioners who are working while studying for qualifications to take more senior roles.
The strike is over a new type of contract which the government says will improve healthcare at night and at weekends but medics say would drastically reduce their pay.
“The new contract is not fair, it’s not safe and from the beginning, we as a profession have been bullied, intimidated and threatened by the Department of Health,” said Florence Dalton, 29, a psychiatrist picketing at St Pancras hospital in central London.
She added that many workers in the state-run National Health Service (NHS) felt “exhausted, overstretched and undervalued”.
“Staff are already leaving in their droves,” she said. “Fewer and fewer people are coming into the profession. It makes me so angry.”
Doctors on several picket lines in London were joined by a choir of NHS doctors and nurses who took this year’s Christmas number one spot in Britain’s pop charts ahead of Justin Bieber with a charity singer.
On Monday, British Prime Minister David Cameron appealed to junior doctors to call off what he said was an unnecessary strike which would cause “real difficulties” to the NHS.
His government says the reforms are needed to help create a “seven days a week” NHS where the quality of care is as high at the weekends as on weekdays.
The NHS has so far postponed 4,000 routine treatments due to the strike.
A further 48-hour stoppage is due to take place on January 26, while on February 10, there will be a full withdrawal of labour from 0800 GMT to 1700 GMT.
The NHS is the fifth largest employer in the world, providing health care which is largely free at the point of delivery.
It is widely respected in Britain, with pollsters YouGov rating it the institution which the most people view positively.