Gasoline direct injection (GDI) and negative valve overlap (NVO) are standard strategies to control combustion characteristics and exhaust gas emissions in homogenous charge compression ignition (HCCI) engines. In this work, experimental data from a single-cylinder engine operated under the GDI-HCCI mode were analyzed. The experiments were performed at an equivalence ratio of 0.95 under a mid-load condition. A side-mounted injector delivered primary reference fuel with octane number 90 directly into the combustion chamber during the NVO. The measured results showed advanced combustion phase CA50 under the early start of injection (SOI) timings. Peak recompression pressures were lower than the motoring, emphasizing that the NVO reactions were net endothermic. Zero-dimensional kinetics calculations showed that classical reformate species increase almost linearly as a function of SOI timings. This work also presents the effects of intake boosting pressure and single versus double pulses injections on CA50, burn duration CA10-90, peak cylinder pressure, combustion noise metrics, thermal efficiency, and emissions. The combustion noise metrics were over the engine constraint limit under advanced SOI timings, but a double-pulse injection could reduce the combustion noise metrics and NOx emission. Late fuel injection in the intake stroke could reduce NOx to a single digit.