"After the appearance of several clinical symptoms and signs, followed by a series of medical examinations and tests, First Lady Asma al-Assad was diagnosed with acute leukaemia," the Presidential office said on Tuesday in a statement.
The statement said she would undergo a specialised treatment protocol that requires her to isolate.
Asma al-Assad, 48, said in 2019 that she had fully recovered from breast cancer.
Last year she accompanied her husband on an official trip to the United Arab Emirates, the first known trip of this kind for her since 2011.
The mother of three children and former investment banker was born in London in 1975 to Syrian parents.
The question had arisen several times in the media as to why she did not leave Syria because of the civil war that began in 2011.
Her husband Bashar al-Assad is accused of war crimes such as the use of poison gas and torture.