The Syrian Observatory for Human Rights was unable to specify the nationality of the aircraft that carried out the raids nor the identity of the slain commander.
The man was killed in a strike on the Ferdaos district, while raids elsewhere in and around the city killed 10, including a child soldier from the ranks of the "Cubs of the Caliphate", said the Observatory.
Raqa is frequently the target of air strikes by the US-led coalition, as well as the Syrian air force and Russian warplanes that began an air campaign in Syria in late September.
Russia stepped up strikes against IS after the group claimed to have downed a Russian passenger plane over Egypt's Sinai Peninsula in October.
At least 32 IS fighters were killed Sunday in apparent US-led air strikes on Raqa province, said the Britain-based Observatory.
Raqa has been under IS control since January 2014 after heavy fighting between the jihadists and opposition fighters, who had seized it from regime control in March 2013.