Welsh ministers said she is "internationally acclaimed" for her work representing children's views through her research.
Prof Holland said she was "delighted and honoured" to have got the job.
She replaces Keith Towler, who is stepping down after seven years.
Prof Holland, director of the Cascade children's social research centre at Cardiff University, said: "Children and young people face new opportunities and challenges in contemporary society.
"I will work with the children and young people of Wales to ensure that their rights are safeguarded and promoted."
FrustrationCommunities Minister Lesley Griffiths said she was confident her "range of experience in social work and children's rights, and her proven commitment to empowering children and young people" would make her a "strong ambassador on their behalf".
Prof Holland is a campaigner for a ban on smacking children and a member of the pressure group Academics for Equal Protection.
The academic will earn between £90,000 and £95,000 a year when she takes up the post in April.
Mr Towler has spoken of his frustration at the delay in naming his successor, claiming the selection process was "less than perfect", and the short handover period was "not great".