One of the major problems of current proton exchange membrane (PEM) fuel cells is water management. The gas diffusion layer (GDL) of the fuel cell plays an important role in water management since humidification and water removal are both achieved through the GDL. Various numerical models were developed to illustrate the multiphase flow and transport in the fuel cell. The accuracy of these models depends on the accurate measurement of the GDL properties such as wettability, surface energy, and porosity. Most of the studies conducted for measuring the wettability of the GDL are based on the external contact angle measurements. However, the external contact angle does not describe adequately the capillary forces acting on the water inside the GDL pores. In a recent study, the capillary penetration technique has been used to measure indirectly the wettability of the GDL based on the experimental height increase due to penetration of the liquid into the porous sample. In essence, the height penetration technique was used along with the general Washburn equation to determine the surface properties of GDLs [Friess and Hoorfar, 2010, “Measurement of Internal Wettability of Gas Diffusion Porous Media of PEM Fuel Cells,” J. Power Sources, 195, pp. 4736–4742]. The shortcoming of this method is that it is only effective for thin GDL samples with low poly(tetrafluoroethylene) (PTFE) loading since the digital images acquired to find the height of penetration has a limited contrast between the penetrated and unpenetrated areas. Since fuel cells need to use different combinations of PTFE loading and thickness depending on the desired use of the cell, it is important to find a way to measure the contact angle of the GDLs with different PTFE loadings and thicknesses. This paper presents a novel fluorescence microscopy method that drastically improves the contrast in the images and allows for the accurate measurement of the height of penetration of the test liquid at each time step. This penetrated height values are then used along with an optimization method (which finds the best fit between the general Washburn equation and the experimental data) to calculate the contact angle of the test liquid on the GDL sample.