The man, whose identity was not revealed, was arrested at dawn on Tuesday in his house at Örebro, about 160 kilometres west of Stockholm.
The suspect came to Sweden in 1998 and was naturalized in 2006. He is suspected of genocide and gross violations of international law, said the prosecutor.
Rwanda's three-month mass killings were triggered by the shooting down of the plane of then president Juvenal Habyarimana, a Hutu, in April 1994.
Sweden sentenced to life imprisonment two other naturalized Rwandans, Stanislas Mbanenande and Claver Berinkindi, in 2014 and 2016 respectively, for their roles in the genocide.
Similar sentences have been handed down in other European countries, the United States and Canada.