A government spokesman said the surgery was successful and a medical report described her as "evolving favorably" in an intensive care unit at a private hospital in Buenos Aires.
The surgery was performed "without complications," the report said.
"It went very well. The president is in good spirits and is already in her room," said undersecretary for public communication Alfredo Scoccimarro.
Kirchner, 60, was diagnosed over the weekend with a "chronic subdural hematoma" resulting from a blow to the head sustained in a fall in mid-August.
More From This Section
Youthful supporters of the president gathered outside the Fundacion Favaloro university hospital where they left flowers and get-well messages around a flag-draped photograph of Kirchner and her late husband Nestor, who preceded her as president.
"Strength, Cristina," "The country and the youth are with you," and "You are irreplaceable," read placards placed at the shrine.
Kirchner has had several bouts of low blood pressure since coming to office in 2007, and underwent surgery in 2012 to remove her thyroid glands after being misdiagnosed as having cancer.
At stake are half the seats in the lower house of Congress and a third of the Senate. Kirchner's Peronist party currently controls both houses, but showed signs of weakness in primaries earlier this year.
Vice President Amado Boudou, a former economy minister from 2009 to 2011, has assumed leadership of the government in Kirchner's absence, although without a formal transfer of presidential powers.