Doctors at Austral University Hospital in Pilar, 40 miles outside the capital Buenos Aires, were able to remove the entire thyroid gland without complications, according to the president's spokesman. The 58-year-old Fernandez is thought to stand a good chance of recovery.
More from GlobalPost: Argentine President diagnosed with thyroid cancer
The Argentine government announced last week that Fernandez had been diagnosed with papillary carcinoma, which was discovered during a routine medical examination before Christmas.
Spokesman Alfredo Scoccimarro said the cancer was on the right side of the thyroid gland, but had not spread to other parts of her body. Specialists say this type of cancer has a high survival rate if treated early.
Well-wishers had been holding vigil outside the hospital since yesterday evening, Reuters reported. There were cheers as the news came that the three-and-a-half-hour operation had been successful, according to the BBC.
Fernandez will remain in hospital for the next 72 hours.
More from GlobalPost: Cristina Fernandez de Kirchner wins re-election in Argentina
Fernandez, who began her second term as president after a landslide election victory in October, is taking 20 days off to re, with Vice President Amado Boudou acting as president until Jan. 24.
Fernandez's election victory came a year after her husband, former president Nestor Kirchner, suddenly died of a heart attack.
During her first term, marked by strong economic growth, Fernandez implemented social policies to benefit the poor, and remains popular, the BBC reported.
Fernandez is one of several Latin American leaders to be diagnosed with cancer – following Venezuelan President Hugo Chavez, Paraguayan leader Fernando Lugo, and former Brazilian President Luiz Inacio Lula da Silva.
Following Fernandez's diagnosis, Chavez, who underwent chemotherapy in Cuba last year, suggested the US might have "developed the technology to induce cancer" in a speech to troops at a military base.