The Football Associations of each country announced the ban on Monday and said a "graduated approach" will be taken to heading in training in under-12s to under-16s football.The ban does not apply to matches because of the limited number of headers which occur in youth games.
The announcement comes after a study showed former footballers were three-and-a-half times more likely to die of the neurodegenerative disease than members of the general population of the same age.
The decision to update the guidelines has been taken to "mitigate against any potential risks", the FA said.
The guidance has been produced in parallel with UEFA's medical committee, which is seeking to produce Europe-wide guidance later this year.
Dawn Astle, who has campaigned for restrictions on heading at all levels of the game, welcomed the news as an important first step.
Her father Jeff Astle was a professional footballer who died in 2002 of chronic traumatic encephalopathy, which the coroner ruled had been caused by repeated heading of a football.
She said: "We must take early steps to avoid exposing children's brains to risk of trauma and by saying there's no heading in training for primary school children is a really sensible way to make the game we all love safer for all those involved."
Professor Willie Stewart, the lead academic on the FIELD study into neurodegenerative disease, also welcomed the move but said ultimately the game's governing bodies must go further.
"A lot more research is needed to understand the factors contributing to increased risk of neurodegenerative disease in footballers," he said.
"Meanwhile it is sensible to act to reduce exposure to the only recognised risk factor so far. As such, measures to reduce exposure to unnecessary head impacts and risk of head injury in sport are a logical step.
"I would, however, like to see these proposals introduced as mandatory, rather than voluntary as present, and a similar approach to reduce heading burden adopted in the wider game of football, not just in youth football."
FA chief executive Mark Bullingham said: "This updated heading guidance is an evolution of our current guidelines and will help coaches and teachers to reduce and remove repetitive and unnecessary heading from youth football.
"Our research has shown that heading is rare in youth football matches, so this guidance is a responsible development to our grassroots coaching without impacting the enjoyment that children of all ages take from playing the game."