Engine correction inputs to control oscillation in an engine output in a transition between 2-stroke and 4-stroke engine cycle modes of an HCCI engine are determined as follows: for each mode, valve timings which modify the engine output the most upon switching are determined, and a linear engine system model is defined at least partially based on the determined valve timings, which model provides mappings relating initial conditions of the engine and the engine correction inputs to outputs of the engine; initial conditions of the engine corresponding to a switching point for switching between the two modes are determined; desired engine output conditions upon switching between the two modes are specified; and the engine correction inputs are determined by using the determined initial conditions, the desired engine output conditions, and the linear engine system model corresponding to the engine cycle mode in effect upon switching.