The NHS staff campaign group Just Health branded the controversial contract “toxic” and unsafe for doctors and patients.
It is arguing that Jeremy Hunt has no legal right to force the new contract on the majority of junior doctors, and that he has not properly consulted all relevant parties.
A letter before action – usually the first step in taking disputes to court – will be delivered to Mr Hunt this morning.
Campaigners took the move after raising £100,000 over four days through a crowdfunding website to bankroll the proceedings.
It heaps further pressure on Mr Hunt, who is also facing a legal challenge from the British Medical Association (BMA) over the contracts.
The BMA is arguing the Government has failed to “pay due regard” to the equalities impact of the new contracts.
Dr Francesca Silman, from Just Health, said: “We hope this legal challenge will hold the Government to account, for imposing a contract that threatens the future stability of the NHS.”
Dr Marie-Estella McVeigh, who is also from Just Health, said: “We feel this contract imposition has been rushed through without appropriate consideration and due process.
“There is no evidence that it will deliver a safer system or better quality care for our patients; it will instead exacerbate the staffing crisis we are already struggling with across the NHS.”
Junior doctors are objecting to a new contract in England which the Government says will create a truly seven-day service.
They are currently paid more for working unsocial hours at night or at the weekend. But under the proposed new contracts, the Saturday day shift will be paid at a normal rate in return for a rise in basic pay.
The dispute has become increasingly bitter and has seen junior doctors go out on strike for the first time in 40 years.
The next is a 48-hour ‘emergency care only’ walk-out from Wednesday April 6 at 8am.
A further 48-hour partial strike was planned from April 26 at 8am but the BMA last month that it will now be a “full withdrawal of labour” from 8am to 5pm on both April 26 and 27.
The move in response to Government’s “continued refusal” to budge on its bid to impose a new contract on trainees by August.
A Department of Health spokeswoman said: “This escalation of industrial action by the BMA is both desperate and irresponsible – and will inevitably put patients in harm’s way.”