The company — which has not traded since Thursday — has not decided whether to appeal the decision. If KaloBios does not respond by Dec. 28, trading in its shares will be suspended on Dec. 30.
KaloBios fired Shkreli on Monday amid allegations of misconduct at his former hedge fund and another pharmaceutical company, Retrophin. He pleaded not guilty to fraud charges Thursday in federal court in Brooklyn, New York, and was released on $5 million bail.
In its decision to delist KaloBios, the Nasdaq cited the arrest and indictment of Shkreli and Evan Greebel, who previously served as the company's outside counsel. Greebel is accused of aiding Shkreli's fraud and has pleaded not guilty.
KaloBios also has failed to file its quarterly report for the period ended Sept. 30.
Shkreli gained notoriety this year when Turing Pharmaceuticals, a company he founded, raised the price of a drug from $13.50 to $750 per pill. He resigned as Turing's CEO on Friday.
Prosecutors say that from 2009 to 2014, Shkreli lost some of his hedge fund investors' money through bad trades. To pay back his disgruntled clients, he allegedly looted $11 million from another pharmaceutical company, Retrophin, where he was CEO.
Shkreli has previously said through his press relations firm said he is confident he will be cleared of all charges, adding that some of the charges involved "complex accounting matters" that authorities failed to understand.
— CNBC's Everett Rosenfeld contributed to this story.