The rally was organised by the British Medical Association (BMA) which claims changes to doctors' working hours would equate to a pay cut for many.
The union said a strike ballot would be held next month.
The Department of Health said the new contracts offered a "fairer, safer deal" for doctors and patients.
Currently, doctors receive a higher rate of pay when they work outside of 07:00 to 19:00 Monday to Friday.
The new deal would see this extended to 07:00 to 22:00 Monday to Saturday, meaning the number of working hours classified as "normal" would be increased by 50%.
The BMA said the contracts, which the government wants to introduce in August 2016, would also remove financial penalties for trusts who overwork junior doctors and cut pay for trainee GPS.
The union said: "The medical profession knows that these changes are unsafe and risk increasing junior doctor burn-out.
"We don't want tired and demoralised doctors."
Junior doctor Peter Campbell told the crowd in Newcastle: "This government is not on the side of the workforce, it is not on the side of the patients, it is ideologically opposed to the founding principles of our NHS.
"This contract is an attack on patients' care, this contract will not just harm our patients but the health of everybody treated by the NHS."
Health minister Ben Gummer said the BMA had "misled" junior doctors over the contents of the contracts, causing "unnecessary anger and upset".
He said: "The great majority of junior doctors will be at least as well paid as they are now and average earnings will remain the same.
"We need safe working hours for NHS staff. The current junior doctors' contract incentivises long hours by offering financial incentives for working beyond the legal limit."
About 4,000 people including many junior doctors have marched through Newcastle to protest against proposed new contracts.