A method of operating a rotary engine including a rotor engaged to a shaft and rotationally received in a housing to define a plurality of working chambers of variable volume, including delivering a pilot quantity of fuel into a pilot cavity in successive communication with the working chambers, igniting the pilot quantity of fuel within the pilot cavity, and delivering a main quantity of fuel into the working chambers downstream of the successive communication of the pilot cavity with the working chambers, where at least one of the pilot quantity and the main quantity is varied between successive rotations of the shaft.