This paper presents a three-dimensional (3-D) computational fluid dynamics (CFD) study of a motored cooperative fuel research (CFR) engine at research octane number (RON) relevant condition. The boundary conditions for 3-D simulations were generated with a one-dimensional GT-Power model. For the first time in literature, a carburetor was added to a virtual CFR engine model with 3-D CFD. Therefore, the proposed setup can simulate the fuel and thermal stratifications inside the engine cylinder with realistic detail. The transient simulations in this work were performed within the Reynolds-averaged Navier-Stokes (RANS) framework with a Realizable k-ε turbulence model. Major conclusions from the present work are: (1) The in-cylinder flow of the CFR engine is swirl-dominated due to the existence of the intake valve shroud. (2) There is a significant amount of liquid droplets entering the cylinder during the intake stroke. The maximum instantaneous amount of liquid for 50% PRF 87 (containing 87% iso-octane and 13% n-heptane (v/v)) and 50% ethanol mixture is indicated to be around 26% of total injected fuel mass. (3) The heat of vaporization (HoV) of the fuel is responsible for creating both temperature and charge stratification inside the cylinder.