Dr Ben White said he was quitting to focus on a legal challenge against the imposition of a new pay and working conditions contract, pledging to fight for the NHS on behalf of patients.
The medic added that there was "not a lot of sense coming from the Government's side of things" ahead of tomorrow's junior doctor strike that will see the NHS's first all-out walkout in history.
Announcing his decision on ITV this morning, Dr White said: "I've taken the decision, or I will do today, to resign as a trainee doctor to focus on a legal campaign, legal proceedings to fight the contract, to fight on behalf of patients and fight for the future of the NHS.
"I feel that I've got an obligation to do that on behalf of my patients."
'Good Morning Britain' presenter Piers Morgan tweeted in shock at the news.
Dr White is one of five junior doctors pursuing a legal challenge in the High Court fighting the contract's imposition, which they claim has “no legal effect whatsoever”.
In a letter to Jeremy Hunt published on Thursday, the 33-year-old medic called for the health secretary to apologise to the public for issuing "damaging weekend statistics and rash advice".
It came as the Royal College of Surgeons president said she would refuse to back the strike if balloted.
Clare Marx told BBC Radio 4's Today programme: "I personally would not countenance a situation where I would be withdrawing my labour, but I know that every single doctor will be thinking very, very carefully about what is involved in this stage.
12,711 non-urgent operations cancelled
45,000 junior doctors walking out
112,856 outpatient appointments cancelled
25,000+ procedures cancelled during previous strikes
"It's a very individual decision: each of these doctors who have been involved in this dispute has been really struggling with their conscience and I think there are many doctors who are having great difficulty in justifying withdrawing labour from emergencies."
One patient who had a spinal operation cancelled for Thursday because of the strike said said she was "desperately disappointed" but still backed the striking doctors.
"We put our lives in their hands these doctors, and our families' lives as well, and they’re a highly educate group of people," Karen Smith told Today.
"If they all say that this contract that's being imposed on them isn't safe then I believe it isn't safe."
British Medical Association (BMA) Chairman Dr Porter Mark Porter claimed later that ministers has "distorted" statistic about weekend deaths and suggested Hunt was ignoring public opinion on the strikes.
He said: "I would look at a Government that has distorted the research and statistics to buttress its non-existent case on this, I would look at a Government that has refused to listen to royal college advice and indeed ignored public opinion on this and I would look around and see the senior doctors who are my colleagues in providing safe care."
He added: "I would also look at a Government that has given junior doctors no choice other than this."
Jeremy Hunt has hit back at the claims doctors are being forced to strike, saying that the upcoming walkout "risks the safety of many patients".
The health secretary has urged the BMA to call off the strike and meet him, but refused to delay the introduction of the new contract as had been suggested in a last-minute cross-party proposal over the weekend.
He wrote to the BMA chairman, suggesting that they meet to discuss other issues affecting doctors such as improvements in training saying :"Next week's withdrawal of emergency care by junior doctors, called by the BMA, seriously risks the safety of many patients who depend on the NHS."
In the letter to Mark Porter, Mr Hunt added: "The extreme action planned will be deeply worrying for patients and place enormous additional strain on our NHS at a time of intense pressure.
"I therefore appeal to you one final time to call off strike action that will see doctors withdraw potentially life-saving care, and to meet with me on Monday to discuss a better way forward."