Police said firefighters worked overnight to extinguish the fire that started today in Orebro, about 160 kilometers west of Stockholm. No one was injured in the blaze.
Mosque spokesman Jamal Lamhamdi told local newspaper Nerikes Allehanda that it was "a sad day for Muslims in Orebro and in Sweden".
As asylum-seekers have flooded into Sweden in recent years, anti-migrant sentiment has grown and there have been increasing xenophobic attacks.
In January, a fire caused major damage at a mosque near Stockholm.
In October, a Syrian man was arrested in an arson attack against a Shiite prayer room in the southwestern city of Malmo.