We report on a systematic study of local structural, magnetic and magneto-optical properties of Mn-doped SiC films synthesized on a 3C–SiC(001) homoepitaxial wafer by an annealing method. A thin Mn layer was deposited on the SiC wafer, and then annealing was performed to diffuse the Mn atoms into the SiC epitaxial layer. Transmission magnetic circular dichroism and magnetization investigations demonstrated ferromagnetic behavior up to 300 K, although the x-ray diffraction studies indicated that the domaint phase of the synthesized layer was antiferromagnetic α-Mn. A detailed extended x-ray-absorption fine structure measurement further revealed that the synthesized sample, in fact, comprises two uncoupled phases: one is the top antiferromagnetic α-Mn layer and the other one is Mn atoms, which may randomly substitute the Si and C atoms in the 3C–SiC lattice. Combining these experimental results with recent theoretical calculations, we strongly propose that the observed room-temperature ferromagnetism was of intrinsic origin, arising from the ’embedded Mn atoms’ in the 3C–SiC lattice, instead of other magnetic clusters.