Heat transfer through the gas diffusion layer (GDL) is a key process in the design and operation of a PEM fuel cell. The analysis of this process requires the determination of the effective thermal conductivity as well as the thermal contact resistance between the GDL and adjacent surfaces/layers. The Part 1 companion paper describes an experimental procedure and a test bed devised to allow separation of the effective thermal conductivity and thermal contact resistance, and presents measurements under a range of static compressive loads. In practice, during operation of a fuel cell stack, the compressive load on the GDL changes. In the present study, experiments are performed on Toray carbon papers with 78% porosity and 5% PTFE under a cyclic compressive load. Results show a significant hysteresis in the loading and unloading cycle data for total thermal resistance, thermal contact resistance (TCR), effective thermal conductivity, thickness, and porosity. It is found that after 5 loading-unloading cycles, the geometrical, mechanical, and thermal parameters reach a "steady-state" condition and remain unchanged. A key finding of this study is that the TCR is the dominant component of the GDL total thermal resistance with a significant hysteresis resulting in up to a 34% difference between the loading and unloading cycle data. This work aims to clarify the impact of unsteady/cyclic compression on the thermal and structural properties of GDLs and provides new insights on the importance of TCR which is a critical interfacial transport phenomenon. (C) 2010 Elsevier B.V. All rights reserved.