Ackman, Pershing Square Capital Management's founder and CEO, first revealed his short position Herbalife in late 2012, but the company's stock has surged 37 percent since then.
He told CNBC on Monday "if you find yourself as an Herbalife employee today, my advice is that you should leave the company because this is not going to be a good thing on your resume. I'd go find another job."
But on Thursday, Herbalife said its talks with the Federal Trade Commission were in advanced stages and could face a payment of about $200 million if the long-running investigation ends in a settlement.
The firm's shares shot up 9.5 percent following the news in Friday trading.
Herbalife also said there are still a number of open issues with the FTC, and the range of possible outcomes includes litigation or settlement.
Ackman's portfolio has also taken a big hit because of its large stake in Valeant Pharmaceuticals, a stock that has shed more than 60 percent in the past three months.
On the flipside, Einhorn's Greenlight Capital revealed a stake in Yelp on Tuesday and the bet is already paying off.
Yelp reported better-than-expected earnings Thursday after the close . On Friday, the stock surged 17 percent.
The company posted first-quarter adjusted earnings of 8 cents per share on $158.6 million in revenue. Earnings dipped slightly from 10 cents per share in the prior-year period, while sales rose about 34 percent from $118.5 million.
Wall Street expected Yelp to post a loss of 16 cents per share on $156 million in revenue.
"We had a great start to the year with local revenue growth accelerating to 40 percent year over year," said Yelp CEO Jeremy Stoppelman, in a statement.
— CNBC's Jacob Pramuk and Everett Rosenfeld contributed to this report.