Fernandez, 58, was easily elected to a second four-year term in October, vowing to deepen her unorthodox policies despite complaints from business leaders who say her heavy-handed management of the economy is stifling investment.
Fernandez was diagnosed with a papillary carcinoma that has not metastasized, said her spokesman, Alfredo Scoccimarro. The operation is scheduled to take place on January 4 and she is expected to take a leave of absence until January 24.
"The thyroid gland will have to be removed," said Buenos Aires-based cancer specialist Julio Moreno. "The prognosis is very good. The chances of being cured are 90 to 98 percent."
The cancer was detected last week during a routine check. Papillary carcinoma is the most common type of thyroid cancer
and normally affects people under the age of 40, especially women.
A skilled orator fond of glamorous clothes, high heels and make-up, Fernandez still wears black as she mourns her husband and closest advisor, former President Nestor Kirchner, who died late last year.
When Kirchner died, many thought it spelled the end of the couple's idiosyncratic blend of state intervention, nationalist rhetoric and the championing of human rights in grains exporting powerhouse Argentina
, the world's No. 3 soybean supplier.
But Fernandez pulled off a remarkable comeback on the back of a brisk economic expansion and an outpouring of public sympathy. She was re-elected with 54 percent of the vote, promising to stay true to her policies despite objections from Wall Street and international investors.
Latin America's No. 3 economy is growing at nearly 9 percent a year. But a worsening global economic outlook combined with entrenched high inflation at home are seen reining in Argentina's growth to about 4 percent next year.
Fernandez is one of several Latin American leaders to have cancer. Venezuelan President Hugo Chavez underwent chemotherapy earlier this year while Paraguayan President Fernando Lugo's lymphatic cancer is in remission.
And former Brazilian leader Luiz Inacio Lula da Silva is being successfully treated for a cancerous tumor on his Larynx, according to his doctors.