Muhammad Mahdi Akif was elected the new guide-general for the Muslim Brotherhood on Wednesday.
Nine out of 15 members of the group's guidance bureau voted for Akif after a controversial secret ballot, said the Islam Online website, which has close ties to the Brotherhood.
The vote came after Mamun al-Hodaiby, the sixth guide-general of Egypt's unofficial opposition, died last week.
Akif, who is a specialist in physical education, joined the Muslim Brotherhood in 1948.
He was sentenced to death on charges of involvement in a failed assassination attempt on Egyptian President Jamal Abd al-Nasir in 1954. The sentence was later commuted to hard labour.
In 1974, he was released from jail and later left for Germany where he ran the group's Islamic centre.
Akif was then elected to the Egyptian parliament in 1981 and remained a member of parliament until 1990.
President Mubarak ''tolerates''
the Muslim Brotherhood
Abd al-Munim Abu al-Futuh, a leading Muslim Brotherhood member, told Islam Online on Monday the group would hold a secret vote to decide a new leader.
The decision was unprecedented as a leader is usually chosen through referenda.
The Muslim Brotherhood was founded in 1928 by Egyptian schoolteacher Hasan al-Banna.
It turned into a political group from 1939 with the principle aim of social and moral reform based upon Islam.
Historically, the Brotherhood has been both close to the government and banned and persecuted by it.
From 1984 it has been accepted as a religious group, but under heavy control by the secular government.
It now disavows violence and campaigns for political change through peaceful means.