The SNSC is responsible for dictating defence and security policies under guidelines set out by supreme leader Ayatollah Ali Khamenei, and for marshalling the country's resources to confront domestic and foreign threats.
Until now, it has been heavily involved in Iran's showdown with world powers over the country's nuclear ambitions, particularly under Rowhani's predecessor, Mahmoud Ahmadinejad.
It is expected that the SNSC's direct involvement will be reduced but not eliminated after Rowhani last week tasked the foreign ministry with taking lead on future nuclear talks.
His performance in the talks and inability to make concession was criticised during the presidential campaign.
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While being replaced as SNSC secretary, Jalili is not expected to leave the council, as he, along with Rowhani, are both special representatives of Khamenei to the council.
Shamkhani, an ethnic Arab, was reformist ex-president Mohammad Khatami's defence minister for two four-year terms until 2005.
His record also includes serving as head of the now-abolished ministry for the Revolutionary Guards under then premier Mir Hossein Mousavi in the 1980s and commanding Iran's naval forces in the 1990s.
In 2000, Shamkhani was awarded the Abdelaziz Second Grade Medal by Saudi Arabia -- whose relationship with Tehran has been tense in recent years -- for his role in "fostering the Saudi-Iranian ties" during the Khatami presidency.