Y-doped BaZrO3 (BZY) is of the perovskite structure (ABO 3), and is promising as an electrolyte in protonic ceramic fuel cells (PCFCs). However, factors limiting its protonic conductivity have not been clarified entirely, such as the unclear site occupancy of Y. In this work, X-ray diffraction patterns were collected utilizing synchrotron radiation with an incident energy close to the energy of the Y K absorption edge. Therefore, precise Rietveld refinement was performed to determine the site occupancy of Y by the anomalous dispersion effect. The results revealed that for the stoichiometric sample of BaZr0.8Y0.2O3-δ, Y only occupied the B-site. But in the Ba-deficient sample of Ba 0.9Zr0.8Y0.2O3-δ, two perovskite phases with different compositions were observed. In the Y-poor phase, all Y occupied the B-site, while in the other greatly Y-rich and Ba-deficient phase, Y was found to occupy both A and B-sites. These results clearly indicate the tendency towards A-site occupation of Y with an increasing Ba-deficiency.