Ruane, Cunniff & Goldfarb’s flagship Sequoia Fund has fallen 28 percent in the last year.

NEW YORK — The CEO of the investment firm with the largest stake in troubled Valeant Pharmaceuticals is retiring after the firm suffered punishing losses from its bets on the drug company.

Ruane, Cunniff & Goldfarb said that Robert Goldfarb would retire and be replaced by David Poppe, co-manager of the firm’s flagship Sequoia Fund.

Bill Ackman’s Pershing Square Capital Management has been the public face of Valeant investor pain. But Ruane, Cunniff & Goldfarb holds a 10.4 percent stake in the company, compared with Pershing’s 9 percent.

That has translated into significant losses for Ruane, Cunniff & Goldfarb, where Goldfarb, a disciple of Warren Buffett, has served as chief executive.

The Sequoia Fund, which was closed to new investors three years ago, has tumbled 28 percent in the last year as Valeant stumbled.

Once a Wall Street star, the Canadian drug company is now besieged by federal probes into its practice of buying companies that own older drugs, than jacking up the prices of the drugs.

Valeant also faces Securities and Exchange Commission investigations, including an inquiry into accounting and inventory issues at Salix Pharmaceutical, a drugmaker that Valeant bought for $11 billion last year.

Last month, Valeant said it would delay filing its 2015 annual report with regulators while it sorts out its former relationship with the mail-order pharmacy Philidor.

On Monday, Valeant announced the departure of longtime CEO Michael Pearson, while Ackman took a seat on Valeant’s board.

Goldfarb has been the co-manager of the Sequoia Fund, which has had an outstanding track record. According to the company, over 45 years through 2015, it has averaged a return of 14 percent per year.

Valeant, however, has taken its toll. The stock has lost 85 percent in the past year.

“While we have beaten the market over the past decade, through the end of 2015, our investment in Valeant has diminished a record that we have built over two generations and in which we take great pride,” Ruane, Cunniff & Goldfarb said in a letter this week. “We are a loyal, dedicated and intensely driven group, and to the extent that we have lost any of our investors’ confidence, we are determined to win it back.”

Those same conversations have been taking place at Pershing Square Capital Management, though Ackman has defended the investment in Valeant.

This week, Pershing reported that its firm had declines of 25.2 percent since January.

Shares of Valeant fell 7 percent Thursday to close at $31.09.