Thin-film Ni–Ca3Co4O9 and Ni–Mo thermocouples were prepared by stepwise magnetron-sputtering/annealing synthesis using masks. Compared with Ni–Mo thin film thermocouples, Ni–Ca3Co4O9 thin film thermocouples have higher output voltage due to large positive Seebeck voltage (153 μV/K for single thermocouple and 912 μV/K for 6-series thermocouple). The maximum output voltage from the thermocouple is 70 mV was obtained for a hot-end temperature of 105 °C for Ni–Ca3Co4O9 for a 6-series thermocouple. The stability of Ca3Co4O9 films and the ability to make free-standing films, together with the high Seebeck coefficient, show that these thin-film oxides can be used as p-type leg in thermocouples, with implications for use in free-standing and flexible thermoelectric devices.