Provided are a substrate processing apparatus and a method of manufacturing a semiconductor device which are able to form a conductive film, which is dense, includes a low concentration of source-derived impurities and has low resistivity, at a higher film-forming rate. The substrate processing apparatus includes a processing chamber configured to stack and accommodate a plurality of substrates; a first processing gas supply system configured to supply a first processing gas into the processing chamber; a second processing gas supply system configured to supply a second processing gas into the processing chamber; and a control unit configured to control the first processing gas supply system and the second processing gas supply system. Here, at least one of the first processing gas supply system and the second processing gas supply system includes two nozzles which are vertically arranged in a stacking direction of the substrates and have different shapes, and the control unit is configured to supply at least one of the first processing gas and the second processing gas into the processing chamber through the two nozzles having different shapes when films are formed on the substrates by supplying the first processing gas and the second processing gas into the processing chamber at pulses having different film-forming rates.