There is significant interest in hydrogen storage systems that employ a media which either adsorbs, absorbs or reacts with hydrogen in a nearly reversible manner. in any media based storage system the rate of hydrogen uptake and the system capacity is governed by a number of complex, coupled physical processes. To design and evaluate such storage systems, a comprehensive methodology was developed, consisting of a hierarchical sequence of models that range from scoping calculations to numerical models that couple reaction kinetics with heat and mass transfer for both the hydrogen charging and discharging phases. The scoping models were presented in Part I [Hardy BJ, Anton DL. Hierarchical methodology for modeling hydrogen storage systems. Part I: Scoping models. Int J Hydrogen Energy 2009;34(5):2269-77] of this two part series of papers. This paper describes a detailed numerical model that integrates the phenomena occurring when hydrogen is charged and discharged. A specific application of the methodology is made to a system using NaAlH(4) as the storage media. Published by Elsevier Ltd on behalf of International Association for Hydrogen Energy.