This paper presents a premixed combustion model based on the first order conditional moment closure (CMC) method for simulation of combustion of iso-octane, which is a single stageignition hydrocarbon fuel under homogeneous charge compression ignition (HCCI) conditions. The model is implemented into the open source C++ computational fluid dynamic (CFD) code known as OpenFOAM. To evaluate the performance of the CFD-CMC solver, a set of direct numerical simulation (DNS) data is used. The data set includes five cases featuring ignition of thermally stratified iso-octane/air mixtures with a mean temperature of 1035 K. The effects of variation of initial temperature fluctuations, turbulence intensity and integral length scale are studied. It is shown that the results from the CFD-CMC solver are in excellent agreement with the DNS for cases in which a low level of conditional fluctuations is present. However, a higher level of these fluctuations leads to an increased deviation of the predicted peak heat release rate and ignition delay time from those of the DNS. A transport equation for the conditional variance is also derived for premixed combustion under HCCI conditions. Assessment of the conditional variance equation using the DNS data shows that correlation between dissipation and conditional fluctuation and correlation between reaction and conditional fluctuations are the dominant sources of conditional fluctuations in the case with a thermal-stratification level of 60 K.