Kirchner was said to be in "good spirits" following the operation yesterday, which came just three weeks before crucial mid-term legislative elections.
A government spokesman said the surgery was successful and a 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 government 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.
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She was hospitalised 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.
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.
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.