Stephen Beadman, 28, is accused of murder and one count of rape.
A second man, Luke Harlow, 27, is charged with grooming and two counts of sexual activity with a child.
The pair, both from George Avenue in the village of Ibstock, Leicestershire, will appear at Leicester Magistrates Court today.
Kayleigh, 15, from Measham in the county, was last seen by her family at around 6pm last Friday when she was dropped off outside Ibstock Community College, in the village.
Police searched extensively for the missing youngster until officers found a body on Wednesday night in undergrowth near a lake in Ibstock.
It was removed from the scene at lunchtime and a post-mortem examination will be carried out to determine the cause of her death.
After the discovery her family said: “We are heartbroken, grief stricken and as a family, utterly devastated. There are no words to express the way we are feeling.
“We cannot even begin to thank the local communities and wider public for their messages of support which have helped us through the last week.
“We are also grateful for the publicity the media have given to Kayleigh’s disappearance and the desperate search to find her.”