The Brotherhood's council elected Mohammad Hekmat Walid for a four-year term in a vote Thursday in Istanbul, where the Syrian opposition in exile is based, a statement said.
Walid, who hails from the regime stronghold of Latakia, is the 12th leader of the Syrian Brotherhood, which was formed at the start of the 1940s but banned in the 1980s after an uprising against Assad's father.
Membership of the Brotherhood is punishable by death in Syria.
Walid has taught at a number of medical schools overseas, including in Ireland and Saudi Arabia.
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Considered the best organised political opposition group, the Muslim Brotherhood, which receives financial support from Qatar, has often been accused critics of seeking to dominate the opposition at the expense of other groups.
The Brotherhood, which is also backed by Turkey, supports Islamist rebel groups in Syria who have lost influence over the past year because of the rise of the Islamic State and other jihadist groups.
The Muslim Brotherhood was founded in Egypt in 1928 by Hassan al-Banna with the goal of an Islamic renaissance and a struggle against the West, a doctrine that then spread to other countries.
In Syria, the movement led an armed uprising against then-president Hafez al-Assad that was brutally crushed in 1982 with at least 10,000 deaths.
Hafez al-Assad was succeeded by his son in 2000.