Savings in other services would pay for it, Health Minister Tony Ryall said.
"This is another example of what can be achieved when you improve efficiency and encourage better performance from the big investment made in health."
District health boards would work with GPs and after-hours clinics to introduce the scheme, starting next July.
"Just as with the daytime free under-6s scheme, there may be some clinics who will not be willing to help young children in this way. DHBs will ensure there are alternatives available within a reasonable distance," Mr Ryall said.
In a media release yesterday, Mr Ryall said free after-hours care would help reduce unnecessary presentations of young children to emergency departments.
After-hours fees for under-6s varied from free to nearly $100, with an estimated average of about $17, Mr Ryall said.
Under-6s were charged $20 at Dunedin Urgent Doctors and Accident Centre, practice manager Martin Chamberlain said.
It was difficult to know whether the scheme would increase demand at the centre, he said. It was not known how many parents would stop attending the Dunedin Hospital emergency department (ED), Mr Chamberlain said.
Mornington Health Centre charged under-6s $20 on week nights, and $30 at weekends, practice manager Barbara Bridger said. Any initiative that helped people receive healthcare was a good thing, she said.
Mosgiel mother-of-two Jackie Gibson said she seldom used after-hours care, but it made sense to provide for young children, who were the most prone to illnesses needing prompt attention.
After-hours charges were tough on parents, especially when long weekends or public holidays meant practices were closed, sometimes for days.
The scheme should reduce pressure on EDs, she said.
Labour health spokesman Grant Robertson said the announcement did not guarantee every clinic would adopt the scheme. Its funding came from other health budget areas, which meant other services were being cut to pay for it.
"Tony Ryall needs to be transparent about what services he'll be stripping as a consequence of not providing extra funding."