Simulation of chemical kinetic processes in combustion engine environments has become ubiquitous towards the understanding of combustion phenomenology, the evaluation of controlling parameters, and the design of configurations and/or control strategies. Such calculations however are not free from error, and the interpretation of model results must be considered in the context of uncertainties within the chemical kinetic mechanism. Uncertainties arise due to structural considerations (e.g., included/missing reaction pathways), as well as incomplete descriptions of kinetic rate parameters and thermochemistry. This study focuses on the latter. Recently, progress has been made toward developing a framework to facilitate uncertainty quantification for a detailed, transportation-relevant fuel model. Under constant volume conditions typical of fundamental apparatuses like rapid compression machines and shock tubes, we have shown, for instance, that variations in ignition delay times can be on the order of a factor of 2–4. This work investigates how kinetic rate parameter uncertainties manifest themselves in terms of combustion phasing under homogeneous charge compression ignition combustion. iso-Octane is used as the fuel under lean fuel loadings (equivalence ratio = 0.35) at naturally aspirated conditions, where a range of combustion phasings is achieved via changes to the bottom dead center (BDC) temperature, covering from near top dead center (TDC) to 18 crank angle degrees (CAD) after TDC. Under this scenario, it is found that the CA50 confidence interval is fairly narrow near TDC (+/- 2.5 CAD, interquartile range), but increases substantially with retarded phasing (e.g., +/- 6 CAD, interquartile range, at 15-degrees after TDC). This trend is caused by a shift in the chemical kinetic regimes that control autoignition timing, where the TDC phasing for this system is modulated by intermediate temperature chemistry, while retarded phasings are influenced by negative temperature coefficient and HO2 chemistry, which are generally less well known and thus have greater uncertainty.