A pilot-scale low-emission boiler system consisting of a bio-fuel boiler and a plasma-chemical hybrid removal system is investigated. This system can achieve carbon neutrality because the bio-fuel boiler uses waste vegetable oil (WVO) as one of the fuels. The plasma-chemical hybrid removal system has two processes: NO oxidation by ozone produced from plasma ozonizers and removal using a chemical scrubber. Test demonstrations of the system were carried out for mixed oils (mixture of heavy oil and WVO). A stable combustion was achieved for the mixed oil (20%–50% WVO). The properties of flue gas—e.g., , , and —when firing mixed oils were nearly the same as those when firing heavy oil for an average flue gas flow rate of 1000 . The concentrations at the boiler outlet were 90–95 ppm. Furthermore, during a 300-min continuous operation when firing 20% mixed oil, a removal efficiency of more than 90% was confirmed. This is equivalent to less than 10 ppm at the scrubber outlet when the flue gas flow rate was 870 . In addition, reduction when heavy oil was replaced with WVO was estimated. The system comparison is described between the plasma-chemical hybrid removal and the conventional removal.