Connor Gibson was also charged with offences relating to the Sexual Offences Act 2009.
A 19-year-old man, who is understood to be the brother of teenager Amber Gibson, has appeared in court charged with her murder.
Amber was reported missing from her home in Hamilton, South Lanarkshire, on Friday.
The 16-year-old’s body was discovered at Cadzow Glen on Sunday morning.
Connor Gibson was also charged with offences relating to the Sexual Offences Act 2009 and with attempting to pervert the course of justice.
He made no plea at Hamilton Sheriff Court and was remanded in custody. He is expected to appear again next week.
A police watchdog has been ordered to examine Police Scotland’s handling of the case, understood to relate to the missing person investigation.
A force spokesman said: “The Crown Office and Procurator Fiscal Service has instructed the police investigations and review commissioner to investigate the circumstances leading up to the death of a 16 year-old girl in Hamilton.”