The 10-minute recording posted on a Web site linked to the terrorist organization, which had yet to be verified as being from al-Zawahiri, came the day before Obama heads to Egypt for a key speech on U.S.-Middle East relations.
The BBC reported al-Zawahiri called Obama "that criminal who came seeking, with deception, to obtain what he failed to achieve on the ground after the mujaheddin ruined the project of the Crusader America in Iraq, Afghanistan and Somalia."
He also lashed out at Egyptian officials who will greet Obama, labeling them "slaves" who have turned Egypt into an "international station of torture in America's war on Islam."
The U.S. network CNN reported al-Zawahiri as saying the American leader showed himself to be an enemy of Muslims by his recent visit to Israel.
"His bloody messages were received and they are still coming and they will not be obstructed either by the public relations campaigns, the shenanigan visits or the articulate words," al-Zawahiri said.