Kathleen Marshall will have been in post for five years in April next year, the term of office for the children's commissioner.
She has said she will not seek to be re-appointed to her role for a second five-year term so a successor will be found by the Scottish Parliament's corporate body.
Marshall said: "It has been a great privilege to be Scotland's first commissioner for children and young people.
"However, I believe ten years would be too long to stay in the post. This seems the right time to step down as it is a natural break and the office is ready to consult on a new set of priorities."
She added: "I hope I have made a difference to the lives of children, especially those whose rights were most under threat such as asylum seekers, children with disabilities and those in care."
During her time as commissioner Marshall has been outspoken in her defence of the rights of asylum seeking children and has submitted several reports on children's rights, including children in prison and children leaving care.
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