More than 5,100 procedures and operations have been postponed as a result of the 48-hour walkout, which began at 8am.
This is the fourth stoppage in the dispute, with almost 25,000 procedures cancelled overall since industrial action began.
Junior doctors will provide emergency care only during the strike, which is expected to hit hospitals hard so soon after the Easter break.
The first full walkout in the history of the NHS by junior doctors is planned for later this month, when doctors will withdraw all labour and provide no emergency cover.
Dr Anne Rainsberry, national incident director for NHS England, said: "We've already seen that a 48-hour strike puts considerably more pressure on the NHS and it's deeply regrettable that thousands of patients are still facing disruption because of this recurring action.
"As always, the safety and care of patients is our number one priority and everything possible is being done to make sure patients will still be able to access urgent and emergency services.
"Following closely on from the four-day Easter break, this will be a difficult period, especially over the course of the second day. Consequently we have redoubled our planning efforts and will be closely monitoring events to make sure we can respond to any rising pressures."
Junior doctors are objecting to a new contract which the Government says will create a truly seven-day service.
The major sticking point has been over weekend pay and whether Saturdays should attract extra "unsocial" payments.
Currently, 7pm to 7am Monday to Friday and the whole of Saturday and Sunday attracts a premium rate of pay for junior doctors.
The Government has said the Saturday day shift must be paid at a normal rate.
The British Medical Association (BMA) also objects to other terms in the contract, which will be imposed from August, but has called on the Government to resume negotiations.
Dr Johann Malawana, chairman of the BMA's junior doctor committee, said: "We deeply regret any disruption this action will cause to patients, but it is because we believe this contract would be bad for the delivery of patient care in the long term that we are taking this action.
"By imposing a contract that junior doctors have no confidence in and refusing to re-enter talks with the BMA, the Government has left us with no choice.
"We want a contract that is fair for all junior doctors - not one which the Government has admitted will disadvantage women - and ensures that they feel valued and motivated so that the NHS can retain the GPs and hospital doctors of the future.
"Responsibility for industrial action now lies entirely with the Government. They must start listening and resume negotiations on a properly funded junior doctor's contract to protect the future of patient care and the NHS."
The BMA is launching a judicial review challenging the lawfulness of the imposition of the contract.
Health Secretary Jeremy Hunt is also facing a second legal challenge from NHS staff campaign group Just Health.
A Department of Health spokeswoman added: "This strike is irresponsible and disproportionate, and, with almost 25,000 operations cancelled so far, it is patients who are suffering.
"If the BMA had agreed to negotiate on Saturday pay, as they promised to do through Acas in November, we'd have a negotiated agreement by now."