Anne Longfield said that youngsters who are spending increasing amounts of time online are not getting the level of support required and called on the Government to take action.
A year-long study into children and the internet, titled Growing Up Digital and published by the Commissioner on Thursday, claims that "much more needs to be done to create a supportive digital environment for children and young people".
Three to four-year-old children spend an of average 8 hours 18 minutes a week online - from watching films to playing games - while 12 to 15-year-olds use the internet for at least 20 hours per week, according to the report.
This "explosion" of time spent online by children has left parents "hoping that bad things wouldn't happen" because they feel they lack the "capabilities or the capacity" to deal with any issues that arise from their child's internet use, meaning children feel they have to navigate the web without parental support, Ms Longfield said.
The study found that children struggled to understand the "impenetrable" terms and conditions of social media sites.
A group of teenagers were asked to read the terms and conditions of photo-sharing site Instagram - used by 56% of 12 to 15-year-olds - as part of the study, but none were able to fully understand what they meant, the report found.
Ms Longfield said: "There was a clear comeback from the kids themselves saying 'I'm staring at the words but they aren't meaningful to me'."
A law firm condensed and simplified the terms and conditions, leaving many youngsters in the study surprised by what they had signed up to.
Ms Longfield has called on the Government to ensure that a search engine's "right to remove" facility - which applies to EU citizens - remains available to children in the UK after Brexit.
She has also urged the Government to appoint a children's digital ombudsman to act as a go-between for children and social media companies.
Speaking to the Press Association, Ms Longfield said there needs to be a "powerful force that's on the side of children" to act as a mediator for them to get content removed from the internet.
The report further suggests that social media companies should rewrite their terms and conditions so that they can be easily understood by children.
As part of the study, 900 Mumsnet users were asked about their worries with children using the internet.
It found that 73% of parents were concerned about their children accessing inappropriate material online and 54% were afraid of unwanted contact by strangers.
"Parents worry about what happens to their children online with regard to strangers and what children worry about online is what happens to them with regard to people they know or come into contact with - which is where bullying begins to really have an impact in terms of children's online presence," Ms Longfield explained.
The recommendations made in the report would give children and young adults the "resilience, information and power" they need to "open up the internet" without making them "vulnerable to having their personal information captured and monetised by companies", it states.
Ms Longfield said: "Kids need to be resilient, they need to have the information ready to be able to deal with their time online and know what that means for them and they need to have the power to deal with it themselves.
"The concern is that the reality of existence for children and teenagers is increasingly spent amount of time online - and their time online is not regulated, it doesn't have adult presence there to support them and they enter that world without the support and resilience they need to be able to know what it entails and how they can manage their time online successfully."
Barnardo's chief executive Javed Khan said: "This report provides further worrying evidence of how children are unprepared to deal with life online and receive little help in dealing with cyber-bullying, 'sexting' and harassment.
"Barnardo's welcomes the call to teach children aged four to 14 how to stay safe online, the dangers of 'sexting' and understand what they're agreeing to when using social media apps.
"With almost a third of 15-year-olds surveyed admitting to sending naked images of themselves at least once, it's vital all children receive compulsory lessons on sex and relationships education, including how to protect themselves online."
A Government spokesman said: "The internet has given children and young people fantastic opportunities, but protecting them from risks they might face online or on their phones is vital.
"The UK is a world leader in internet safety, but there is more to do, and we will carefully consider this report as part of our ongoing work to make the internet a safer place for children."