The 30-year-old Orlando Pride forward, one of the most prominent players on the United States' World Cup-winning team, made the announcement in a statement on her Instagram account.
"This year has had the highest of highs but along with that comes challenges and sometimes even falling short of my goals I set for myself in 2019," Morgan wrote.
"I'm disappointed I won't be able to compete with the Pride for the remainder of 2019 due to a knee injury I've been managing since the World Cup, and that I can't be there to help my teammates and my club have more success. "I have already started physical therapy in LA and am eager to get back on the field doing what I love."
Morgan did not release further details of her injury.