A substrate processing method capable of preventing a reduction in productivity of the fabrication of a semiconductor device from a substrate. An HF gas is supplied toward a wafer having a thermally-oxidized film, a BPSG film, and a deposit film, to thereby selectively etch the BPSG film and the deposit film using fluorinated acid. A residual matter of H2SiF6 produced at the time of etching is decomposed into HF and SiF4 by being heated.