The American drug maker will pay $830 million to investors who bought Merck securities between 1999 and 2004.
The lawsuit stemmed from statements Merck made about the cardiovascular safety of Vioxx.
Vioxx was withdrawn from the market in 2004 after evidence showed it doubled the risk of heart attack and stroke.
In 2011, Merck pleaded guilty to federal charges of violating marketing laws related to its sale of Vioxx.
Federal officials accused Merck of making false statements and illegally marketing Vioxx as a treatment for rheumatoid arthritis to increase sales.
The company said this latest settlement with investors did not constitute an admission of guilt by the drug maker.
Merck still faced a number of individual lawsuits related to Vioxx.
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