The research and development of graphene and graphene-based materials have been significantly increasing since they were invented. However, in many industries, the applications of graphene nanoflakes are still few, compared with other materials. This study presents the fabrication of highly conductive graphene thin film (GTF) papers to reduce the possible damage of lightning strikes on composite structures. Three concepts were presented in this project: (1) fabrication of a highly conductive functionalized nanosize GTF, (2) incorporation of the GTF into carbon fiber-reinforced composite panels, and (3) introduction of 3D stitching concepts into composite structures to protect against the effects of lightning strikes. Experimental studies have shown that the highest electrical and thermal conductivity values measured on GTF papers are approximately 1,800 S/cm and 425 W/m.K, respectively. After GTF was incorporated into the carbon fiber-reinforced composites, some delamination was observed between the GTF and the composite. Therefore, the 3D stitching concept was introduced to reduce this delamination. Four stitch configurations with different stitch lengths, thread-to-thread thicknesses, thread tensions, and thread thicknesses were used. Then, tensile tests were carried out on the prepared unidirectional fiber composite test coupons. Although the delamination was completely eliminated, tensile strength on some of the test configurations was reduced. This study will be useful in increasing the electrical and thermal conductivity values of composite surfaces in aircraft and wind energy industries.