The group is advising youth coaches to remove drills involving headers from all training sessions, and also recommends heading "as far as possible, is also eliminated from games".
It comes after a recent study suggested former footballers are approximately three-and-a-half times more likely to die from neurodegenerative disease than the general population.
"As far as possible, heading the ball during games at this age group should also be avoided.
"The SYFA has previously recommended against training drills that encourage repetitive heading of the ball.
"However, in light of Dr Willie Stewart's recent study into dementia risks in former professional footballers, we have updated and strengthened the advice to our clubs.
"We would also take this opportunity to remind all of our coaches and officials that if any player, at any age group, is suspected of having a concussion they must immediately cease playing in the game and should not re-join the match.
"Coaches and officials are reminded of NHS advice on concussion and head injury, and should seek immediate medical advice if symptoms continue or worsen, or if a player is suspected of having lost consciousness.
"As well as the continuation of our own work in this area, we are keen to engage in further discussions with Dr Stewart around his findings and will continue to work closely with the Scottish FA to make any additional recommendations.
"Although there is not yet a definitive link between heading the ball and brain injury, it is essential that we take the relevant precautions to best protect our players."
Dr Stewart's study focused on the medical records of 7,676 men who played professional football in Scotland between 1900 and 1976 which were matched against more than 23,000 individuals in the general population.
His findings reported the "risk ranged from a five-fold increase in Alzheimer's disease, through an approximately four-fold increase in motor neurone disease, to a two-fold Parkinson's disease in former professional footballers compared to population controls".
A ban on heading for under-12s is to be considered by the Scottish Football Association (SFA).
Other potential measures by the SFA include tighter guidelines on heading practice, ensuring age-appropriate ball sizes are being used, and guidance to grassroots coaches.
In the United States, a ban is in place on heading for children under 10, and it is limited in training sessions for those aged 11-13.