Dye-sensitized solar cells are promising solutions to energy and environmental problems. By addressing the high cost of preferred platinum counter electrode, Co/Se and Ni/Se nanocomposite counter electrodes are prepared by magnetron sputtering targets onto fluorine-doped tin oxide glass for dye-sensitized solar cell applications. The binary nanocomposite counter electrodes exhibit superior electrocatalytic activity toward I-3(-) reduction compared to pure Ni, Se and Co electrodes. In particular, the dye-sensitized solar cell based on Co/Se counter electrode achieves a power conversion efficiency of 6.43%, which is much higher than 0.87%, 2.91%, 3.77% and 5.23% for Ni, Se, Co and Ni/Se solar cells, respectively. The preliminary results demonstrate it is a promising strategy to prepare robust counter electrodes by magnetron sputtering technique for dye-sensitized solar cells.