The prediction of the effective thermal conductivity of composites filled with carbon fibers requires the knowledge of the microstructure, the relative amount and thermal properties of filler and matrix materials, the orientation of non-isometric filler phases and the thermal contact resistances between fibers and matrix and also between fibers. However, information at small scale are often missing especially thermal contact resistances. The present work describes the measurement of the thermal contact resistance (TCR) between two crossed carbon fibers which is performed by an adaptation of the T-type 3ω method for thermal conductivity measurement of wires. The first carbon fiber is connected to two copper blocks supplied by a modulated electrical current providing a volumetric heating. The second fiber fixed on a U-shape holder is delicately implemented over the first one. After performing a secondary vacuum, the 3ω voltage V3ω of the first fiber is recorded as function of the frequency of the modulated current. Knowing the applied force, the contact area between the two carbon fibers is calculated from bending and deformations then a 3D numerical model describing heat transfer in two crossed carbon fibers is used to estimate the TCR at their intersection. In addition, a detailed sensitivity analysis of the unknown parameter TCR is performed allowing to find optimal operating conditions especially the frequency range. Measurements are performed with PAN type carbon fibers (FT300B) picked up from the same bundle. Different TCR estimations were performed by fitting numerical and computed V3ω voltage as function of frequency. Finally, values of TCR between crossed carbon fibers were found equal (10.4 ± 10.1) 105 kW−1 which provides an order of magnitude for such phenomenon.