According to one embodiment, a substrate processing apparatus includes a first liquid supplier, a second liquid supplier, and a controller. The first liquid supplier supplies a substrate with a sulfuric acid solution having a first temperature equal to or higher than the boiling point of hydrogen peroxide water. The second liquid supplier supplies a surface to be treated of the substrate with a mixture of sulfuric acid solution and hydrogen peroxide water having a second temperature lower than the first temperature. The controller controls the first liquid supplier to supply the sulfuric acid solution so as to heat the substrate to the boiling point of hydrogen peroxide water or higher. When the temperature of the substrate becomes equal to or higher than the second temperature, the controller controls the first liquid supplier to stop supplying the sulfuric acid solution and controls the second liquid supplier to supply the mixture.