The approval makes Lilly's Effient the first real competition to the blood thinner Plavix, the world's second-best selling medication made by Sanofi-Aventis and Bristol-Myers Squibb.
The FDA delayed its decision on Effient multiple times during an 18-month review, as agency staffers weighed the drug's benefits versus its risks.
A study of over 13,000 patients conducted by Lilly found that Effient prevents more heart attacks than Plavix, but also causes more internal bleeding.
The FDA said Effient will carry a boxed warning to alert physicians to the risks of "significant, sometimes fatal, bleeding." The boxed warning is reserved for issues that can cause serious injury or death.
The drug should not be taken by patients with a history of bleeding, stroke or who are undergoing surgery, the FDA said.
"Physicians must carefully weigh the potential benefits and risks of Effient as they decide which patients should receive the drug," said Dr. John Jenkins, FDA's director of new drugs.
The drug offers an alternative treatment for preventing dangerous blood clots that can lead to heart attack or stroke, Jenkins said.
The boxed safety warning could curb sales, but not to a large extent, according to Miller Tabak & Co. analyst Les Funtleyder.
"The FDA has been a lot more liberal with black box warnings than it was in the past, and in a way the black box has lost some of the meaning it had when it was rare," said Funtleyder. "But it still has the ability to somewhat limit sales."
Company studies showed 7 percent of patients taking Effient experienced nonfatal heart attacks, compared with 9.1 percent of patients taking Plavix. Despite lower rates of certain heart attacks, the actual rates of death were similar for both drugs.