A model-based control strategy to track combustion phasing during load and speed transitions in the homogeneous charge compression ignition (HCCI) operating region of a multimode combustion engine is presented in this paper. HCCI transitions can traverse regions of high cyclic variability (CV), even if the steady state transition end points are stable with low CV. A control-oriented HCCI model for both the stable, low CV region and the oscillatory, high CV, late phasing region is used to design a controller that uses valve and fuel injection timings to track combustion phasing. Novel aspects of the controller include nonlinear model-inversion-based feedforward and gain scheduled feedback based on unburned fuel that reduces transient CV. Transitions tested on a multicylinder HCCI engine include load transitions at fixed engine speeds, simultaneous load, and speed transitions, and select FTP75 drive-cycle transitions with high load slew rates. Good combustion phasing tracking performance is demonstrated, and misfires are prevented.