HCCI engines have mainly focused on achieving low temperature combustion in order to obtain higher efficiency and lower emission. One of practical difficulties in HCCI combustion is to control the start of combustion and subsequent combustion phasing. The choice of primary reference fuels in HCCI strategy is one of various promising solutions to make HCCI combustion ignition-controlled. The behavior of ignition delay to the frequency variation of sinusoidal velocity oscillation is computationally investigated under HCCI conditions of PRF75 using a reduced chemistry in a counterflow configuration. The second-stage ignition is more delayed as the higher frequency is imposed on nozzle velocity fluctuation whereas the first-stage ignition is not much influenced.