"Ms Elisabeth Borne today submitted the resignation of the government to the president, who accepted it," the presidency was quoted as saying by the France 24 broadcaster.
Macron thanked the outgoing prime minister for her service.
"Madam prime minister, dear [Elisabeth Borne], your work in the interest of our nation was exemplary every day. You implemented reforms with courage, commitment and determination. I thank you with all my heart," the president wrote on X.
Borne will continue to perform her duties as France's prime minister until her successor is appointed, the France 24 broadcaster reported.
French Defense Minister Sebastien Lecornu might become the new prime minister of the country, the report said, adding that Finance Minister Bruno Le Maire and Ecology Minister Christophe Bechu were also among the possible candidates.