A computer simulation model has been developed to aid in the understanding, parameter prediction, and performance optimization of a unique dialysis process where glycerol is removed from cryopreserved red blood cells using a semipermeable membrane pouch fixed in a mildly agitated transport cell. The dynamic system considered here consists of flow channels and the membrane blood pouch which contains the red blood cells, extracellular fluid, and cryopreservatives. Dialysate flows over the membrane surfaces while salt enters the pouch preventing osmotic hemolysis. The glycerol diffuses rapidly from the red cells and plasma across the membrane into the dialysate which carries it out of the transport cell. The system is discretized into completely mixed subdomains. Constituent transport and solvent flux are modeled with the transient convection-diffusion equation and linear equations of nonequilibrium thermodynamics, respectively. The integrated compartment method was used to solve for the principal variables, that is, salt and glycerol concentrations, water flow rates, and pressure in space and time. The computer simulation model, calibrated and verified with in-house data sets, is a reliable, cost-effective and flexible tool for dialysis system investigations, prediction, and optimal design.