A medical report said Kirchner, 60, was instructed to observe "strict rest for 30 days" and told to avoid air travel until further notice.
"Due to the favourable post-operative evolution of the president, it has been decided to discharge her today," the report said.
Presidential spokesman Alfredo Scoccimarro told reporters Kirchner would be leaving the hospital "in a few minutes."
She was to spend her convalescence at Los Olivos, the presidential residence on the outskirts of Buenos Aires.
The hematoma, which was recently detected, was from a blow to the head suffered in a fall in mid August.
The medical setback comes as the country heads into mid-term legislative elections October 27 expected to set the tone for Kirchner's final two years in office.