KaloBios, which has a market cap of less than $100 million, hasn't traded since last Thursday. It was halted about 10 minutes after news of Shkreli's arrest.
The company said the alleged fraudster was "terminated" as CEO, and he resigned from his post as a member of its board.
The 32-year-old former hedge fund manager pleaded not guilty Thursday in Brooklyn federal court and was released on $5 million bail.
He was charged with securities fraud and conspiracy. Prosecutors say from 2009 to 2014, Shkreli lost some of his hedge fund investors' money through bad trades, then looted a pharmaceutical company where he was CEO for $11 million to pay back his disgruntled clients.
Shkreli was already widely reviled because a different drug company he founded raised the price of a life-saving drug from $13.50 to $750 per pill. He resigned as the company's CEO on Friday.
—The Associated Press contributed to this report.