Recently experiments were conducted on an automotive homogeneous-charge-compression-ignition (HCCI) research engine with a negative-valve-overlap (NVO) cam. In the study two sets of experiments were run. One set injected a small quantity of fuel (HPLC-grade iso-octane) during NVO in varying amounts and timings followed by a larger injection during the intake stroke. The other set of experiments was similar, but did not include an NVO injection. By comparing both sets of results researchers were able to investigate the use of NVO fuel injection to control main combustion phasing under light-load conditions. For this paper a subset of these experiments are modeled with the computational-fluid-dynamics (CFD) code KIVA3V [ 6 ] using a multi-zone combustion model. The computational domain includes the combustion chamber, and intake and exhaust valves, ports, and runners. Multiple cycles are run to minimize the influence of initial conditions on final simulated results. The goals of this study are to validate the CFD model under NVO, HCCI-like conditions, evaluate assumptions made in the experimental study, and provide further insight into the thermal and chemical effects associated with NVO fuel injection.