The seminars will be run by the Association of School and College Leaders (ASCL) in major English cities.
New legislation passed this year places a statutory duty on schools and colleges to counter radicalisation.
The seminars will be led by Kamal Hanif, head of Birmingham's Waverley School and an expert on Islam and citizenship.
The union says the aim is to offer support and guidance to senior school leaders in the wake of high-profile cases such as that of the three London schoolgirls who travelled to Syria in February and are believed to be in the city of Raqqa, a stronghold of Islamic State.
Their families later complained that police, the school and the local authority had failed to pass on information they said could have prevented the girls leaving.
The Counter Terrorism and Security Act 2015 requires educational establishments to prevent young people being drawn into terrorism.
The seminars, in June and July, will help school and college leaders understand these duties and give them practical help and advice.
The aim is to maintain an atmosphere of equality and diversity in schools but also to help teachers understand how social media can be used "to groom young people into extremist ideologies", says the union.
"This is about having a greater understanding around the issues of radicalisation and extremism," said Mr Hanif.
He said the seminars would help head teachers "identify situations" and "deal with them in an appropriate manner, without overreacting and being alarmist.
"Young people spend a lot of their time on the web and social media and they can easily get drawn into extremist ideas without access to a counter-narrative.
"These seminars will help schools and, in turn, parents, who often have no idea that their children are accessing this sort of information, to pick up the signs, and use the appropriate channels in dealing with these concerns.
"They will help to equip heads with the counter-narratives to some of the false claims put out by extremists."
Mr Hanif  will be joined by the counter-extremism campaigner Sara Khan, co-founder of the counter-extremism and women's rights organisation Inspire  and by ASCL's parliamentary specialist Anna Cole.
Ms Khan said the seminars would clarify what schools were expected to do.
"Unfortunately, there has been a great deal of myth propagated about what the statutory requirements mean for both schools and pupils."
Ms Cole said the aim was to avoid criminalising young people by helping schools intervene "in the right way at an early stage".
"The key thing is to put in place proper risk assessments and have an open culture where different views and ideas can be discussed in an open way.
"We want to reassure schools that these steps will help them meet the statutory requirements and protect young people."
The seminars in Bristol, Birmingham, Cambridge, London, Manchester, Leeds and Durham will be open to ASCL members and non-members.
Head teachers worried about protecting students from being radicalised are being offered seminars by a union.