This study focuses on the characterization of transverse deformations, particularly through-thickness deformations, in 3D re-entrant hexagonal composite structures reinforced with fibrous materials. Given the lack of prior research on fiber-reinforced composites with this particular geometry, a measurement method based on digital image correlation (DIC) is proposed. By utilizing stereo-DIC, it becomes possible to measure the thickness variation of the sample and, consequently, its out-of-plane deformation. Experimental tensile tests were conducted on a thermoformed composite sample comprising a 4 × 4 array of re-entrant cells, with a 2 × 2 central region analyzed in detail. The sample was subjected to cyclic tensile loading, revealing a deformation homogenization phenomenon despite loading conditions designed to remain within a macroscopically linear elastic response range. A methodology for processing the experimental measurements is proposed, supported by numerical simulations to validate its accuracy. This approach aims to refine the experimental protocol and data processing techniques for samples exhibiting fewer manufacturing defects and material heterogeneities than the prototype used for method development. Furthermore, the numerical study enhances the understanding of the deformation mechanisms specific to the investigated re-entrant hexagonal composite unit cell.