Sarepta Spokesman Ian Estepan said in a written statement to CNBC, "This is an internal FDA matter and therefore not appropriate for us to comment."
The FDA did not immediately respond to CNBC's request for comment.
Earlier in the session, shares had jumped more than 15 percent. On Tuesday, investment firm Oppenheimer said in a note that it found Farkas has left the agency and is no longer listed on the U.S. Department of Health and Human Services employee directory.
"We view this as a positive signal for eteplirsen approval," analyst Michelle Gilson, who gave the stock an "outperform" rating, said in the note. She added the firm believes the FDA has already made a decision on the drug.
The FDA deferred its decision on whether to approve the drug and asked Sarepta for more trial data in June.
In April, NBC News reported Farkas said he was not trying to keep a good drug off the market but was keen on looking at the data in different ways. He added that he and other experts could not tell whether the patients tested were being helped by the drug.
Jim Cramer told CNBC's "Squawk on the Street" Wednesday that he thinks the news is a sign the FDA will give approval for the drug.
"This is a terrible disease," he said. "A lot of the parents of the people who had this went to the FDA and said listen, 'The safety profile is fine. Please give us something.'"
Even with Wednesday's gains, Sarepta's stock is down more than 15 percent this year-to-date.