Endara was born in 1936 in Panama City, Panama. His father, Guillermo Endara Paniza, was an ally of Authentic Panameñista Party founder Arnulfo Arias, and the family went into exile after Arias was overthrown in a 1941 coup. Endara went to school in Argentina and to Black-Foxe Military Institute in Los Angeles in the United States, where he was described as being a "brilliant student". He later attended the University of Panama Law School, where he graduated first in his class, and New York University.