It is the outfielder's second monthly award, with the other coming in May, making Harper the first Nationals rookie to earn multiple monthly awards in a single season.
Harper, 19, led the Majors with 26 runs in September, and ranked second in the NL in slugging percentage (.651) and total bases (69). His seven home runs and 35 September hits also led all NL rookies, while his .330 average ranked second.
He also had seven doubles, three triples and drove in 14 runs while stealing four bases.
Harper posted his second career multihomer game on Sept. 5 and knocked a career-high four hits on Sept. 11, one of 11 multihit games in September. He ended the month by hitting his 22nd homer, the second-highest single-season total in Major League history for a teenager.
Harper's 97 runs this season already rank as the most by a rookie in franchise history.