She follows in the footsteps of Matildas teammates Katrina Gorry (2014) and Caitlin Foord (2016) in winning the honour.
Former Socceroos mentor Ange Postecoglou missed out in the coach's category.
Kerr, who plays club football for Perth Glory in Australia and Sky Blue in the United States, finished ahead of Japan's Saki Kumagai and Sung Hyang-sim of North Korea.
"A lot of Australians have previously won the award, so I'm very humbled to win not only because the Australians have done well but also because it's a great award and I'm very excited," Kerr said.
"It's been a bit of a crazy year."
The honour caps off an incredible season for the 24-year-old who was also shortlisted for the FIFA womens' player of the year award.
Kerr found the back of the net a record 17 times this season for United States based National Women's Soccer League side Sky Blue FC, setting a new all-time league scoring record with 43 goals in the process.
The Fremantle product has also excelled on the international stage to spearhead the Matildas surge to sixth in the FIFA world rankings, scoring eleven goals in her past six matches.
Postecoglou and Japan's Masatada Ishii were pipped by Ishii's countryman Takafumi Hori.
Socceroos midfielder Aaron Mooy also missed out on the International Asian Player of the Year Award.
Awarded to Asian players plying their trade outside the confederation, the gong went to Tottenham midfielder Son Heung-min.
The 25-year-old Son helped Spurs finish second in the Premier League last season, scoring 14 goals. He also helped South Korea qualify for a ninth straight World Cup.
Omar Khrbin, part of the Syria side who faced the Socceroos in September's Asian World Cup play-offs, became the first player from his nation to be crowned Asia's Player of the Year.
The 23-year-old claimed the title ahead of last year's winner, Omar Abdulrahman of the United Arab Emirates, and China's Wu Lei, who missed out for the second year in a row.
