The 18-time Grand Slam singles champion, who previously had breast cancer in 2010, will start treatment in New York later this month.
“The double whammy is serious, but fixable, and I’m hoping for a favourable outcome,” she said. “It’s going to stink for a while, but I’ll fight with all I have got.”
Navratilova noticed an enlarged lymph node in her neck during November’s WTA Finals in Fort Worth, Texas.
A subsequent biopsy revealed stage one throat cancer.
During the tests, a lump was also discovered in her breast, which was later diagnosed as an unrelated cancer.
“Both of these cancers are in their early stages with great outcomes,” Navratilova’s representative Mary Greenham added.
Navratilova was due to cover this month’s Australian Open from the Tennis Channel studio in Melbourne, but will instead make some occasional remote appearances.
The nine-time Wimbledon singles champion said she felt “helpless” after she was diagnosed with cancer in 2010, but decided to go public with the news to help other women suffering similar health problems.
By Russell Fuller
BBC tennis correspondent