An etchant composition, and methods of patterning a conductive layer and manufacturing a flat panel display device using the same are provided. The etchant composition may include phosphoric acid, nitric acid, acetic acid, water and an additive, wherein the additive includes a chlorine-based compound, a nitrate-based compound, and an oxidation regulator. In addition, the flat panel display device may be manufactured by patterning a gate electrode, source/drain electrodes and a pixel electrode using the same etchant composition. The gate electrode, source/drain electrodes and the pixel electrode may be formed of different conductive materials. Accordingly, processes are simplified so that manufacturing costs may be reduced and productivity may be improved.