NHS staff campaign group Just Health branded the controversial contract "toxic" and said it was unsafe for doctors and patients.
The group is arguing the Health Secretary has “no legal power to impose the Junior Doctors contract on the majority of doctors,” and says he has not properly consulted all relevant parties.
Just Health raised £100,000 over four days through a crowdfunding website to bankroll the proceedings
The challenge will place 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 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, 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 which they would be required to work more weekends and lose extra pay on Saturday in exchange for a basic pay rise of 13.5 per cent.
The Government says the new contract will create a truly seven-day service on the NHS. Medics say the changes will incentivise unsafe shift patterns, putting patients' safety and lives at risk.
The dispute has become increasingly bitter and has seen junior doctors go out on strike for the first time in 40 years.
Mr Hunt's contract has also been criticised by the director of the World Health Organisation (WHO), who says it contradicts the status of women set out by the United Nations.
The Government's own Equality Impact Assessment of the imposed contract acknowledged it will "impact disproportionately on women".
Strike action planned for late April will see junior doctors stage a full walk-out for the first time.
Additional reporting by PA
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