Mr Hunt said on Twitter that he was delighted to remain in the 'best job in government', and that reports of his death had been 'greatly exaggerated'.
'Reports of my death have been greatly exaggerated...' Thrilled to be back in the best job in Government.— Jeremy Hunt (@Jeremy_Hunt) July 14, 2016
The decision to keep the health secretary in his DH role comes just days after junior doctors voted to reject a new contract.
Mr Hunt said last week the vote had left the NHS in 'a no-man's land' and that the only remaining option was to impose the deal.
Junior doctor strikes
Almost six out of 10 junior doctors rejected the deal, raising the prospect that hostilities could resume in the long-running dispute that led to a wave of unprecedented strikes in recent months.
Earlier indications that Mr Hunt would be removed from his DH post came in a tweet from a senior BBC journalist.
Jeremy Hunt also out— Laura Kuenssberg (@bbclaurak) July 14, 2016
Mr Hunt's tenure as health secretary has totalled three years and 305 days. He is already the longest-serving health secretary since role took its current form in the 1980s, and the fourth longest-serving of any minister in the lead health role since the NHS was created.
Reacting to confirmation that Mr Hunt would remain in post, BMA chairman Dr Mark Porter said: 'We remain committed to continuing our work with Mr Hunt on the development of health policies to assure the quality of patient care.
'There are extremely difficult decisions ahead and doctors need to play a central role in shaping the delivery of healthcare. More than ever we need a period of stability and a working environment that encourages partnership and co-operation.
'We also still need to agree a contract for junior doctors in which they have confidence and I urge Mr Hunt to build on the progress that has been made so far to address outstanding issues and regain trust from junior doctors, who are the future of the profession.
'We need a long-term strategy that addresses the workload and funding challenges that are overwhelming the NHS. Doctors want to see the secretary of state put the NHS on a sustainable footing for the future, address the serious funding shortfall and ensure we can recruit and retain the right number of doctors that our patients desperately need.'