We investigated the effect of annealing temperature on magnetic properties of 2% and 10% Fe-doped BaTiO3. To understand the possible structural differences between samples treated at different annealing temperatures, and to correlate them with the magnetic properties, several characterization techniques, such as X-ray diffraction and X-ray absorption spectroscopic methods (XANES and EXAFS) were employed. We found that the 2% Fe-doped BaTiO3 pseudocubic perovskite is paramagnetic regardless of the heat-treatment conditions. Initially paramagnetic 10% Fe-doped 6H–BaTiO3, treated at 1250°C, became ferromagnetic after additional annealing at higher temperature. We have crystalographically characterized the cation ordering processes in the 6H–BaTiO3 that occurred during the high-temperature annealing. The ferromagnetism that is induced in this stage is most probably associated with the observed diffusion processes but it extrinsic character still cannot be fully disregarded.