The man was charged on Friday after having been convicted in his absence in Rwanda for involvement in the country's 1994 genocide, the Stockholm prosecutor's office said.
The suspect, who had lived in Sweden since 2002 and was naturalised in 2012, is suspected of being a low-level official involved in the murders, attempted murders and kidnappings of Tutsis.
His trial opens on September 16th and is due to end in March.
He was sentenced in 2007 in absentia to 30 years behind bars by the Rwandan authorities who later tracked him to Sweden, where Swedish officials opened an inquiry.
Prosecutor Tora Holst told the AFP newswire that the suspect, who was placed in detention pending trial a year ago, could not be expelled to Rwanda because he was now Swedish.
Under Swedish law a suspect can be remanded in custody while a prosector gathers evidence to bring charges.
According to the UN, some 800,000 people died in the Rwandan genocide, which began after the assassination of Rwanda's Hutu president Juvenal Habyarimana two decades ago.