The sector has suffered from headline risk on the campaign trail ever since Clinton tweeted that she plans to tackle "price gouging" in the pharmaceutical industry.
Buyout chatter and optimistic trial results had initially boosted the sector.
The IBB was helped by shares of Sarepta Therapeutics and Incyte, which had gained as much as 9 percent and 7 percent, respectively. Those stocks have since pared their gains. Sarepta ended the day slghtly lower while Incyte was still modestly higher on the day.
In early trading, Insys Therapeutics shares jumped as much as 12 percent after the company reported statistically significant results for a phase 3 trial of its Sublingual Buprenorphine Spray. The study found that patients that used Insys' product had the greatest reduction in pain.
Insys CEO John Kapoor said that the company's "Buprenorphine Sublingual Spray could be a potentially useful drug for the treatment of moderate to severe pain and provide a valuable treatment option in a variety of clinical settings." Kapoor also said Insys will discuss the results with the FDA by the end of the year and is moving towards filing a new drug application.
After Clinton's tweet, Insys shares gave up their gains and ended the session 4 percent lower.
Shares of PharMerica also surged 13 percent after Reuters, citing people familiar with the matter, reported that the U.S. pharmacy manager is exploring strategic alternatives, including a potential sale.
— CNBC's Chris Hayes contributed to this report.