In an effort to advance the knowledge and understanding of biodiesel combustion characteristics in compression ignition engines, computational fluid dynamics (CFD) modeling has been utilized to study the in-cylinder physical and chemical events. The development of combustion kinetics and thermophysical properties of biodiesel in CFD modeling is crucial, since both of these govern the in-cylinder combustion and emission formation processes. As such, this review reports on the advances attained within three key aspects of CFD modeling of in-cylinder biodiesel combustion. The key aspects are surrogate chemical kinetic mechanisms, mechanism reduction methods, and biodiesel thermophysical properties models. Because of the complex fuel compositions, combustion modeling of biodiesel fuel largely depends on the surrogate chemical kinetic mechanisms. Recent developments in biodiesel chemical kinetic mechanisms have shown a progression from small detailed mechanisms toward large detailed mechanisms. The main challenge facing in-cylinder biodiesel combustion modeling is the limited data available for validation of the modeling results. In order for biodiesel surrogate mechanisms to be coupled to CFD modeling, it is necessary to reduce the detailed mechanisms to manageable sizes. A number of methods are currently available for this purpose, each with its own advantages and disadvantages as reviewed here. However, detailed understanding of these reduction methods is necessary before any reduction work is carried out. In addition to the reaction kinetics in the surrogate mechanisms, successful simulation of the in-cylinder biodiesel combustion using CFD is dependent on the thermophysical properties of the fuel. The models used to determine these thermophysical properties for CFD studies, as reported in the literature, are also appraised.