Two major hospitals in Leicester and London told to stop providing complex heart surgery are now being allowed to continue, NHS England has announced.
But patients in Manchester will now have to travel to Liverpool.
The decision comes after a lengthy process to reorganise congenital heart services in England after new standards of care were introduced in 2015.
The services are for people born with heart problems, such as holes in the heart.
Congenital heart disease is the most common birth defect, affecting between five and nine in every 1,000 babies born in the UK.
Units providing specialist care for these heart problems, at University Hospitals of Leicester NHS Trust and Royal Brompton and Harefield NHS Foundation Trust, had been under threat of closure because they were not meeting the new standards.
They include the requirement that surgeons work in teams of at least four and do at least 125 operations a year each to ensure they keep their skills up-to-date.
But after a public consultation, NHS England bosses said they had changed their minds.
However, they said the decision was conditional on both hospitals achieving "full compliance with the standards".
Manchester University Hospitals NHS Foundation Trust will no longer be able to provide surgery for complex congenital heart disease patients, but it will be allowed to offer less complex care.
Liverpool Heart and Chest Hospital will now provide the most complex heart care for adults and children in the north-west of England.
NHS England also said Newcastle upon Tyne Hospitals NHS Foundation Trust would continue to be allowed to provide complex congenital heart disease services until at least 2021.
While the changes could mean some patients travelling further than they previously needed to, NHS England says the care that would be provided would be safer in the long-term.
Prof Huon Gray, national clinical director for heart disease at NHS England, said: "Every patient should be confident that their care is delivered by a hospital that meets quality standards, which have been developed after long consultation with patients, their families and specialist clinical staff."
He said progress towards meeting the standards so far had been "encouraging", but there was more work to do to achieve this within the timescales set out.