The Irish Medical Organisation is to hold a one-day national strike of non-consultant hospital doctors on Wednesday 25 September.
The protest over working hours follows a ballot of NCHD members in which 97% of 1,000 doctors voted for action.
The union has also announced that each week from 30 September a strike will be called in at least one hospital in each region in the country.
The union has promised that emergency services, oncology and dialysis will not be affected.
It is serving three weeks' notice of the action on the HSE and both sides will meet tomorrow to discuss contingency measures.
The IMO represents around 2,000 of the 4,800 junior doctors in the health system.
The union is calling for an immediate end to shifts in excess of 24 hours.
The HSE says that many large hospitals have made significant progress towards compliance with the European Working Time Directive on a 48-hour-week for doctors, but there are problems in small to medium sized facilities.
NCHD Committee Chairman Dr John Donnellan said: "This has been an extremely difficult decision for doctors to make and we would not be in this position were it not for the inaction and prevarication of the Department of Health and the HSE.
"Even now, the Minister for Health could resolve this issue by directing his colleagues to tackle this issue once-and-for-all."