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14 August 2017, 06:00 | Updated: 14 August 2017, 06:33
Almost one in five parents chose bullying as their key worry, while pupils' mental wellbeing, the cost of uniforms and getting children back into the school routine also ranked highly, Action for Children Scotland found.
The findings were drawn from a poll of 1,000 parents of five to 16-year-olds who will be going to school this August.
Just over 18% chose bullying as their biggest concern, while almost 10% opted for mental health and wellbeing.
More than 14% of those surveyed were most concerned about the cost of new school uniforms, while 16.6% were most worried about switching back into the school routine.
Around 9% were most concerned about the transition from one school year to another, or from primary to secondary.
The parents, who were questioned by pollster One Poll between July 31 and August 9, were also asked about the factors which would make the biggest difference to pupils' school experience.
Almost 16% chose one-to-one support, around 18% chose peer mentoring, while just over 19% said after school clubs and classes would make the biggest difference.
Action for Children Scotland said the survey results highlighted the need for parents to talk to their children regularly, monitor use of social media and build in family time when young people and children are more likely to open up about their problems.
Paul Carberry, director of the charity, said: "We want starting the new school year to be a positive, exciting time for children and their parents.
"Our staff are on hand to provide practical and emotional support to help with the transition back to school, recognising the range of challenges that some families face.
This includes bringing parents and teachers together to resolve difficulties jointly and at an early stage."
The charity has also welcomed the Scottish Government's Pupil Equity Fund which can be used directly by schools on measures to reduce the poverty-related attainment gap.
Mr Carberry added: "The Pupil Equity Fund is a real opportunity to make a difference to those children who are at greatest risk of non-attainment, and to bring in flexible support to help address the challenges."