Offenders can face decades of stigma in addition to serving prison or juvenile detention sentences, the report says.
The laws cover offences from the very serious, such as rape, to consensual sex between minors and public nudity.
The report says there is no evidence that listing youth offenders on such registries improves public safety.
Some of those on the registry were listed for offences committed while they were as young as 10 years old, says Human Rights Watch.
The Raised on the Registry report says that publicly listing under-18-year-olds who commit sexual offences violates their rights, so US authorities should exempt them from such registers.
"Many people assume that anyone listed on the sex offender registry must be a rapist or a paedophile," said Nicole Pittman, author of the report. "But most states spread the net much more widely."
In some cases, known as statutory rape cases, children can be added to the sex offender registry for having consensual sex with a peer or a child below the age of consent.
It cites the example of Alexander D who was convicted at the age of 17 of criminal sexual misconduct for having sex with his 15-year-old girlfriend. In the state of Michigan, the legal age of consent is 16.
Alexander has lost jobs and been called a "paedophile" for appearing on the register. His name will remain there until 2028, despite letters from his girlfriend's parents to have his name removed.
Moreover, the report says that in many states failure to register is a criminal offence that could result in fines or imprisonment of up to 10 years.
In two cases cited in the report, youths were convicted of sex offenses at 12 and committed suicide at 17 due to what their mothers said was despair because of their listing on the registers.
One young offender, Connor, told Human Rights Watch he has had to register since the age of 13.
"I was shaking when I went to the sheriff's office to register," he said, according to the report.
Listed for 'Sexting'
Human Rights Watch says that in many cases the restrictions imposed on those registered are unnecessarily onerous, and can limit where and with whom youth sex offenders can live, work, go to school or spend time.
Those that do have to register should be regularly reviewed and be allowed to provide evidence of rehabilitation, or a change in living circumstances, the report says.
However, the National District Attorneys Association said it would not support a blanket exemption of juveniles from the sex offender registers.
Its executive director, Scott Burns, said prosecutors should have the discretion to require registration or not on a case-by-case basis.
"If a 15-year-old 'sexted' a picture of him or herself, it is safe to say that prosecutors would take appropriate steps to ensure that person isn't required to become a registered sex offender for life," Mr Burns told the Associated Press news agency.
"If a 17-year-old had committed multiple violent sex offences against children, registration as a sex offender would most likely be recommended."