The "full withdrawal of labour" will take place across England during the working day from 8am until 5pm, and it is expected that further strike action will take place.
But what is the strike about and how will it affect patients?
What is the strike about?
Currently the Government wants to create a seven-day NHS, but according to the British Medical Association (BMA) "the Government has no answer to how it will staff and fund extra weekend care".
The BMA has said junior doctors had been left with "no choice" but to start fresh strike action after failed attempts to resolve the remaining issues with the contract.
With just weeks to go before a new contract is imposed on junior doctors by the Government, the BMA say that "time is running out".
The BMA added that union members felt the contract did not do enough to reward those who work the most weekends, was unfair on part-time workers and there was strong opposition to the fact that it was being forced on them.
Were the last strikes successful?
What is the imposed contract like?
Under the contract which the Government will impose on junior doctors, they would see a basic pay rise of between 10% and 11% on average.
Those who work one in two weekends would get an extra 10% on top of basic pay, while night shifts would attract an extra 37%.
Under the old system junior doctors were paid anything between 20% and 100% extra for weekends or night shifts worked.
When will the strikes take place?
If talks between the Department of Health and the BMA are successful and the new contract is not imposed then the strikes will be called off.
If not, junior doctors will stage a "full withdrawal of labour" between 8am and 5pm, between September 12 and 16.
Emergency care will still take place.
It is expected that further strike action will take place.
How will the strikes affect patients?
The Department of Health is urging patients to chose the right services for them, and to only use Accident & Emergency departments if it is "absolutely essential".
While A&E will still be open services may be more stretched than usual.
If a patient has an operation or procedure booked for one of the strike dates they will be contacted by their hospital advising them what will happen.
If you fear you may be affected and want further advice, contact the Patients Association on 0208 423 8999.