Bruce Adamson said the former first minister had let families down over child poverty and mental health.
Mr Adamson, who stands down next week after six years in the role, criticised ministers for delays to adopting the UN Convention on the Rights of the Child.
The Scottish government said it was committed to making Scotland the "best place in the world" for young people.
In an interview with BBC Scotland's The Sunday Show, Mr Adamson said the children most at risk were not receiving the support they needed.
"We have to focus on children's rights, all of the things they need to thrive," he said.
"An adequate standard of living for all children in Scotland, to have a safe, warm home, good nutritious food and the right clothes to wear.
He said Scotland's young people still did not have access to the highest standard of health and mental health, or education that developed them to their "fullest potential".
He added: "When government is making decisions around things like funding - around free school meals and mental health counselling in schools - there's some real failures there.
"When we see cuts to things like youth work, early years services, that scaffolding around families it raises some really serious concerns.
Ms Sturgeon said she was proud of her legacy for young people when she stood down as first minister in March.
Mr Adamson acknowledged that she did a "really good job" keeping people safe during the Covid pandemic, but said Ms Sturgeon had hugely challenging role and had "absolutely" failed young people.
"The pandemic had a huge impact on children's rights," he said.
"It had a disproportionate impact on those who were already most at risk, that's the really concerning thing.
"Children who were in poverty, disabled children, young carers, they were most impacted by the pandemic.
"We really need a step change in the way that we address those concerns, by putting funding in to those support services, in order to get that early and effective support."
Mr Adamson said he was not confident that Ms Sturgeon's successor Humza Yousaf would do better for young people.
He said: "I think the new first minister may have made some big promises, but we've not seen anything on delivering those."
The children's commissioner also said there had been "a year and a half of prevarication and delay" over the UN Convention on the Rights of the Child.
In 2021 the Scottish Parliament backed incorporating the UN convention into Scots Law.
However, a Supreme Court challenge from UK law officers said the legislation could affect Westminster's ability to make laws for Scotland.
Scottish Ministers have still to make the required amendments that would allow a bill to pass.
"It's the most important thing we can do in legal terms to improve children's lives," Mr Adamson said.
"It will improve the way we can hold those in power to account, when we fail to deliver for children on things like housing, support on education, on mental health - where we know we're not doing well enough."
The Scottish government has pledged to amend the legislation and bring it back to Holyrood, but no timescale has been given.
A spokesperson said ministers were committed to making Scotland "the best place in the world to grow up" and reducing poverty in young people.
They said the UN Convention on the Rights of the Child was a "critical piece of legislation" ministers were determined to bring back to parliament "as soon as practicable".
The Scottish Conservatives said Mr Adamson's comments were a "devastatingly brutal assessment" of how ministers had failed Scotland's children.
The party's spokesperson for young people, Meghan Gallacher MSP, said: "In this area, as in so many others, the actions of the SNP government fall dismally short of their grand words."
Scottish Labour children's spokesman Martin Whitfield said Mr Adamson had punctured the SNP's "empty spin" on young people.
"Child poverty has persisted, the attainment gap remains and care-experienced young people are not getting the support they need," he said.
Scottish Lib Dem leader Alex Cole-Hamilton said Humza Yousaf "must completely reboot the SNP's agenda" and acknowledge that his party had "comprehensively failed children and young people".