An autonomous canister vacuum cleaner has a cleaning head module, a vacuum fan module separated from the cleaning module, and a hose assembly connecting the cleaning head module with the vacuum fan module. The vacuum fan module includes a controller that performs navigation and control functions for both the vacuum fan module and the cleaning head module. Alternatively, the controller may be separated from the vacuum fan module and the cleaning head module, and can be mobile. The vacuum fan module and the cleaning head module each include a drive mechanism for propulsion. The cleaning head module includes a cleaning brush assembly that can be motorized or air driven. The cleaning head module may also include a microcontroller that communicates with the controller.