In this study, we developed a comprehensive model to simulate vacuum gas oil (VGO) hydrocracking. The model incorporates knowledge of feedstock composition and reaction chemistry at the molecular level and is tuned with pilot plant data. The molecular makeup of the feedstock is derived from its analytical characterization via statistical modeling. Hydrocracking reactivity is described based on the molecular structure of the reactants. Progression of chemical reactions is simulated using a kinetic Monte Carlo algorithm. A stochastic heat balance equation is integrated into the model to represent adiabatic operation. Vapor liquid equilibrium (VLE) calculations are executed in parallel with an inhouse flash program. Hydrocracker simulations were conducted covering the typical range of conversion levels observed in commercial operation. The model generates detailed information on product distribution as well as product quality. In addition, the model is able to track the evolution of hydrogen consumption, hydrocarbon vaporization, and temperature along the reactor.