Ten-year-old Engla Juncosa Höglund went missing in April this year after her bike was found in the woods only 500 metres from her family home in Darlarna.
After a huge search operation, Anders Eklund was arrested when his car and the girl on her bike were photographed within minutes of each other on the same road.
When later confronted with DNA evidence, the 42-year-old also confessed to the murder of Pernilla Hellgren in Farun in 2000.
Eklund is also charged with the rape of a minor, child pornography offences and the rape of another woman in 2006.
The trial begins in Stockholm district court on Monday.