A government spokesman said on Tuesday 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.
60-year-old Kirchner was diagnosed over the weekend with a "chronic subdural hematoma" resulting from a blow to the head sustained in a fall in mid-August.
She was hospitalized on Monday after experiencing tingling in her left arm and muscle weakness, prompting her doctors to order surgery to drain the hematoma lodged between the brain and its outer casing.
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.
The current medical setback comes at a sensitive political moment, with Argentines going to the polls October 27 to cast ballot in legislative elections that will set the political direction for the country halfway through Kirchner's second and last term.
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.
Boudou visited Kirchner Monday night in the hospital, after he announced at an official event that she had asked him to keep the government running.
Kirchner herself has not been seen in public since the government announced on Saturday that doctors had ordered her to rest for a month.
Anders Cohen, head of neurosurgery at the Brooklyn Hospital Center in New York, told AFP the procedure that Kirchner was to undergo was a common operation that can be done safely anywhere in the world.
"It is a short hospitalization, maybe three days, and then a rehabilitation. For a return to full duty, it is from four to six weeks," Cohen said.
He said Kirchner's prognosis should be good.
He said an incision is made in the cranium, and an opening is made - a procedure that lasts about 45 minutes.
The accumulated blood is then removed and surgeons ensure there is no bleeding left before installing a drain, which Cohen said patients usually tolerate well.
Accompanying Kirchner at the hospital is her son Maximo, 36, and her mother Ofelia Wilhelm.
Her sister-in-law Social Development Minister Alicia Kirchner also visited her, and messages wishing her a speedy recovery came in from fellow South American presidents.
Meanwhile, experts debated the constitutional and political implications of Kirchner's condition.
Daniel Sabsay, an expert on Argentina's constitution, said that if Kirchner were unable to perform the duties of her office, "the correct thing would be to ask Congress for leave and transfer powers to the vice president."
It now falls to Boudou to lead the governing party's campaign to keep control of the Congress, but analysts say he is the least popular member of Kirchner's team.
The 50-year-old Boudou is under investigation for alleged influence peddling on behalf of a graphics company, although no charges have been filed in the case.