Recently, electromagnetic interference (EMI) shielding materials have absorbed a lot of attention due to a growing need for application in the area of electronic and wireless devices. In this study, a carbon-based EMI shielding composite was fabricated by electrophoretic deposition of Fe3O4 nano-particles on carbon fibers (CFs) as a 3D structure incorporated with an epoxy resin. Co-precipitation method was employed to synthesize Fe3O4 nano-particles. This as-synthesized Fe3O4 nano-powder was then successfully deposited on CFs using a modified multi-step electrophoretic deposition (EPD) method. The results of structural studies showed that the Fe3O4 nano-particles (25 nm) were successfully and uniformly deposited on CFs. The measured magnetic properties of as-synthesized Fe3O4 nano-powder and nano-Fe3O4/CFs composite showed that the saturation magnetization of bare Fe3O4 was decreased from Ms = 72.3 emu/g to Ms = 33.1 emu/g for nano-Fe3O4/CFs composite and also corecivity of Fe3O4 was increased from Hc = 4.9 Oe to Hc = 168 Oe for composite. The results of microwave absorption tests revealed that the reflection loss (RL) of an epoxy-based nano-Fe3O4/CFs composite are significantly influenced by layer thickness. The maximum RL value of −10.21 dB at 10.12 GHz with an effective absorption bandwidth about 2 GHz was obtained for the sample with the thickness of 2 mm. It also exhibited an EMI shielding performance of −23 dB for whole the frequency range of 8.2–12.4 GHz.