ISLAMABAD, Pakistan—Ex-President Pervez Musharraf was charged in court with a role in the 2007 assassination of former Pakistani Prime Minister Benazir Bhutto, his most serious legal setback since his return to the country in March.

The onetime military ruler was charged in a Pakistani antiterrorism court on Tuesday with criminal conspiracy and facilitation of murder, lawyers said. Mr. Musharraf pleaded not guilty.

Ms....