The man, 19, is accused of murdering Ida Johansson, who was found dead in the Stockholm suburb of Runby in August in a high-profile case that sparked a nationwide debate about the safety of solo runners.
He confessed to killing the woman a month later, but denied murdering her.
In an indictment on Monday, Attunda district court said that he had been formally charged with murder, aggravated rape and treating a dead person in a disrespectful way and that he would face a trial next year.
The defendant's lawyer, Sofia Björksten, told Swedish newspaper Dagens Nyheter that the man was suffering from mental health problems when the attack took place.
“He felt mentally ill at the time, that much I can say,” she argued.
Björksten has asked for a closed session for the trial, without journalists, due to the nature of the allegations and the defendant's age. Her application will be considered by the court.
The search for Johansson's killer was extensive, seeing police comparing the DNA of over 800 men with traces found at the crime scene.
The man set to face trial, who was not known to police previously and has not been named by the Swedish media, was caught by police after a witness placed him at the scene on the night of the crime. A DNA test confirmed that he had been in the area at the time of Johansson's death.
Just days after the woman was found dead, thousands of people took to tracks across the Nordic country in the much-publicized 'Run with love' campaign to pay tribute to Johansson – and to show defiance in the face of fear.