Iodine deficiency (ID) can result in irreversible damage to the brain during the fetal and neonatal stages. As the active center of many enzymes, trace elements play essential roles in brain function. In this work, the relative contents and distributions of elements (Cl, Br, Fe, Cu, and Zn) in two important brain regions, the cerebral cortex and hippocampus, of the iodine-deficient model rats were determined by the synchrotron radiation X-ray fluorescence (SRXRF) method. Meanwhile, the ID rats were supplemented with adequate and excessive iodine, respectively. The results indicated that the distributions of trace elements could be influenced by the different iodine intakes in the stage of brain development. In contrast to the control group, the contents of Cl, Br, and Zn in two brain regions showed a significant increase in the ID group; however, both Fe and Cu decreased in the cerebral cortex and increased in the hippocampus in the ID group. In addition, only slight changes of elemental contents in brain were found between the adequate and excessive iodine-supplemented rats.