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The 24-times capped England international injured her knee and has since undergone surgery, but is expected to be back in action by April.
Duggan was an integral member of the City side that won the Continental Cup against Arsenal last season.
"It’s always difficult to when you're out of action, but these things happen in football, and hopefully I’ll be back playing soon," said Duggan. "I'd like to thank everyone for the messages of support I've received and the procedure went well."
MCWFC begin their second season against Birmingham on 29 March.