The 30-year-old was injured at a Chelsea training camp in January.
Matildas coach Tony Gustavsson announced a squad for Australia’s pre-Olympic friendlies, stating that Kerr would not be able to return in time for the July Games.
Kerr, probably Australia’s most famous athlete, is the country’s all-time leading goalscorer.
She joins a lengthy line of high-profile female footballers who have suffered ACL injuries, including England captain Leah Williamson and Dutch striker Vivianne Miedema. Professional athletes typically require at least nine months to return to full fitness following surgery.