Having made the initial ten player preliminary list, the in-form forward missed the cut when the nominees were trimmed to three.
The winner will be one of American midfielder Carli Lloyd, the Netherlands' Leike Martens or Venezuela's 18 year-old striker Deyna Castellanos after they were announced as the definitive trio.
The Matildas have been in superb form, having won their last six matches with Kerr playing a vital role, scoring a hat-trick against Japan at the Tournament of Nations, before netting three goals in two matches in the two-game series against Brazil, only making Kerr's omission even more surprising.
The 24 year-old won the Julie Dolan Medal for best player in the W-League during the 2016/17 season, scoring 10 goals as she helped lead Perth Glory to the grand final where they went down to Melbourne City before continuing her form overseas where she became the National Women's Soccer League's leading scorer, while equaling the record for most goals in a single season with 16.
The Australian Footballer of the Year's omission surprised many in the football world, including her Matildas teammates.