She was on a shortlist to direct Marvel's first female superhero movie, Captain Marvel, but likely will be out of the running for that role now.
Her appointment will help improve Disney's problems with diversity. A recent report showed that only five out of 101 movies from the studio were directed by women.
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Mulan is the latest in a long line of Disney remakes of its classic animated features, following the success of The Jungle Book and Cinderella.
It will be based on the 1998 animated musical, which starred Ming-Na Wen, Eddie Murphy and George Takei. It was based on the Chinese legend of Hua Mulan, a woman who took her father's place in the Chinese army.
The Hollywood Reporter, which broke the news of Caro's appointment, report that to help with cultural authenticity, Hong-Kong based producer Bill Kong has signed on as executive producer. Kong has worked on movies such as Crouching Tiger, Hidden Dragon.
Disney is also working with cultural consultants, and is focusing its search for the movie's stars in mainland China.
The studio tried to hire an Asian director for the position, and approached Ang Lee and Rogue One star Jiang Wen, both of whom turned down the position.
Caro came to international attention for directing Whale Rider in 2002, which launched the career of Kiwi actress Keisha Castle-Hughes.
She went on to direct Charlize Theron in the legal drama North Country.
Her next movie, The Zookeeper's Wife starring Jessica Chastain, is set for release in New Zealand cinemas on May 4.
Mulan is scheduled for release in November 2018.