Levi Bellfield, 41, will be charged with kidnapping the 13-year-old as she walked home from school eight years ago before killing her.
The former doorman and wheelclamper, originally from West Drayton, Middlesex, will appear in custody before Staines Magistrates’ Court on April 13.
He will also be charged with attempting to kidnap 12-year-old Rachel Cowles the day before Milly disappeared.
Amanda Dowler, known to her family as Milly, disappeared while walking home from school in Walton-on-Thames, Surrey, on March 21, 2002.
Six months later her skeletal remains were found 50 kilometres away by mushroom pickers in Yateley Heath, Hampshire.
Her parents, Bob and Sally Dowler, thanked detectives for their “painstaking work” over the past eight years.
“It’s very hard to say how we feel after eight long and difficult years.
“We are extremely grateful to Detective Superintendent Maria Woodall and her investigating team for their painstaking work and support to us over the years.
“We are pleased that Levi Bellfield has been charged with abduction and murder and hope this will go some way towards providing justice for our darling Milly.”
Bellfield was interviewed over Milly’s death five years ago after he was held by the Metropolitan Police.
Bellfield was living with his girlfriend Emma Mills a short distance from where Milly was last seen.
A red Daewoo Nexia, owned by Ms Mills, was caught on CCTV driving away from area at about the time Milly disappeared.
The car has never been recovered by police.
A similar car was involved in the incident the previous day in which a 12-year-old girl was offered a lift home in Shepperton.
This event is understood to be what lies behind the first charge, an allegation that Bellfield attempted to kidnap Ms Cowles.