Children in P6 and P7 will learn how to cope with change under the Healthy Me programme developed by Northern Ireland charity, Action Mental Health.
Its chief executive David Babington said it will help prepare pupils for the stresses of the transfer test and big changes in their educational life.
Five schools took part in a pilot.
The charity is now hoping the programme will be rolled out in schools across Northern Ireland.
It consists of "interactive workshops" in which pupils are made aware of the importance of emotional wellbeing; encouraged to seek help if they are in distress and helped to identify sources of support.
The workshops also provide teachers with basic training in promoting emotional wellbeing.
The Healthy Me initiative was launched at Carrick Primary School in Lurgan, County Armagh, on Friday morning.
The school's pastoral care co-ordinator, Helen Hamilton, is also its P7 teacher and said the programme has helped pupils and parents ahead of the big move.
"I see the anxiety in kids starting to build about secondary school," Ms Hamilton told BBC News NI.
"No fault of the secondary school - they're excellent and many are very excited to be going there - but they're apprehensive too and a lot of the time, that can be fed down from parents as well, they're worried about them.
"You're going from a very close-knit family atmosphere in a primary school - where you have one teacher who sees a child every day all day, and gets to know them and their wee quirks and can spot very quickly if they're out of sorts - to the very difficult job of senior school teachers who see them maybe for half an hour.
"It's more difficult for them to pick up on those things, much as they try, so parents sometimes need the reassurance and understanding that the transition can be easier than they expect."
Getting a place in a secondary school can be source of stress however, and last month, thousands of P7 pupils began to sit this year's unofficial transfer tests, set by two different examination bodies, the Association of Quality Education (AQE) and GL Assessment.
Pupils have the choice to sit either test, both tests, or none, but figures provided to the BBC by the two organisations indicated a slight rise in the number of entrants sitting the tests this year, with a total of 14,681, a rise from 14,575 in 2015.
"Transition from primary to secondary school is a particularly stressful time for children and we believe that targeting the programme at P6/P7 children will help them cope with this transition," Mr Babington said.
"Modern life is stressful and can impact on mental health, so implementing strategies for protecting children from stress and helping them learn to cope with change is an extremely positive influence on their young lives," the Action Mental Health boss added.
Ms Hamilton said that in the workshops, children were taught breathing exercises, and "how to relax", including how to take time out from busy after-school activity regimes.
"We, as a school, value so much the amount of evidence that shows that children who, mentally and emotionally, aren't ready to learn cannot progress, so   it's so important for us that children's social and emotional needs are met," the P7 teacher added.
The need to "strengthen the resilience of young people" is one of the key challenges facing Northern Ireland's education system, according to the chief inspector of schools, Noelle Buick.
"All young people need to build resilience," she wrote in her  latest report, published last month..
The chief inspector said pupils were facing "complex challenges" because the "social context of relationships, values, attitudes and behaviours in which children and young people live and learn has changed significantly" in recent years.
"It is timely to review the need for strengthening the resilience of children and young people at all levels through stronger and more explicit preventative education within the wider taught pastoral care curriculum."
Pupils preparing to leave primary school are being taught how to deal with stress and to be more resilient as part of a new mental health initiative.