The son of former United captain Wayne Rooney, Kai - at 15 years of age - has been part of the U18 team this season.
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However, he took to social media to post an image of himself wearing a protective boot on his right foot.
In a caption overlaying the photo, he wrote: "Life can't get worse" alongside a crying emoji.
For now, there is no news on the extent of the injury or how long he will be missing.
Kai has been with the United academy since the age of 11.