In this study, we aimed to investigate whether chronic shift in light/dark cycle alters brain trace element concentrations. For this purpose, 20 male Wistar albino adult rats were weighed and randomly divided into three groups. The first group (n = 6) was the control and had been subjected to 12/12-h light/dark cycle for 30 days. The second group (n = 7) was subjected to 6/18-h light/dark cycle for 15 days, and the third group (n = 7) was also subjected to 6/18-h light/dark cycle for 15 days and then returned to normal 12/12-h light/dark cycle for 15 days. When light/dark cycle protocols were completed, tissue specimens of the frontal lobe, temporal lobe, and brain stem were collected. Iron (Fe), zinc (Zn), and copper (Cu) concentrations of the frontal lobe, temporal lobe, and brain stem were determined by an atomic absorption spectrophotometer. When compared with controls, Fe levels of the temporal lobe significantly increased in 6/18-h light/dark cycle group (p < 0.05), whereas it was statistically unchanged in rats which were exposed to 6/18-h light/dark cycle then returned to the normal 12/12-h light/dark cycle period. Our results show that chronic shift in light/dark cycle affects trace element concentrations of the brain, especially Fe level in the temporal lobe, and these changes are reversible.