James Watson, of no fixed address, was charged with the 1994 murder on Monday following a decision by the Bedfordshire, Cambridgeshire and Hertfordshire Major Crime Unit to reopen the case.
The boy’s naked body was found in woodland a few minutes walk from his home in Redmile Walk, Welland, Peterborough, on 29 November 1994.
A post-mortem examination concluded that Rikki, who had disappeared after leaving home to walk to school, had been strangled.
His uniform was found dumped in a nearby bin.
Mr Watson, who was a child at the time of the murder, will appear at Peterborough Magistrates’ Court on Thursday.
Rikki’s mother, Ruth, was originally accused of killing her son in 1995 and denied the charge.
She was later cleared of the murder but was instead found guilty of child neglect and cruelty, and jailed for seven years.
For more than two decades, no one has been convicted over the child’s death.
In 2014, police decided to review the cold case and began reinvestigating in 2015.
“Following the death of Rikki Neave in Peterborough in November 1994, the Crown Prosecution Service has today authorised Cambridgeshire Constabulary to charge James Watson, 38, with murder. Rikki Neave’s family have been informed,” Chief Crown Prosecutor Chris Long said in a statement.
“This decision was made following careful consideration of all the evidence presented to us by Cambridgeshire Constabulary as a result of their cold case review and subsequent lengthy and complex investigation.”
Ruth Neave said in 2018 she wanted to do everything in her power to “get justice” for her son.
“It has had an awful effect on the family. They hate me but it was not me who killed Rikki, so they should blame that person – not me,” she told Cambs Times.
“When Rikki died, I died. Something inside me died, it felt like having my arm ripped off.”
Additional reporting by PA