The suit was filed Monday in federal court against Delta and Atlantic Southeast Airlines Inc.
It said Masudur Rahman and Mohamed Zaghloul went through several security checks. It claims the pilot wanted them off the plane because he thought their presence would make other passengers uncomfortable. The men are described in the suit as having beards and "traditional Arabic clothing." It seeks compensation for losses and injuries as well as punitive damages.
Atlantic Southeast and Delta issued a statement condemning discrimination but declining to comment further.
The two were traveling to a conference on anti-Muslim discrimination.