COBRA-SFS (Spent Fuel Storage) is a general thermal-hydraulic analysis computer code used to predict temperatures and velocities in a wide variety of systems. The code was refined and specialized for spent fuel storage system analyses for the US Department of Energy's Commercial Spent Fuel Management Program. The finite-volume equations governing mass, momentum, and energy conservation are written for an incompressible, single-phase fluid. The flow equations model a wide range of conditions including natural circulation. The energy equations include the effects of solid and fluid conduction, natural convection, and thermal radiation. The COBRA-SFS code is structured to perform both steady-state and transient calculations: however, the transient capability has not yet been validated. This volume describes the finite-volume equations and the method used to solve these equations. It is directed toward the user who is interested in gaining a more complete understanding of these methods.