An interior ministry statement also classified two jihadist groups fighting with the Syrian rebels – the Nusra Front and the Islamic State in Iraq and the Levant – as terrorist groups.
A royal decree issued last month said any citizen found guilty of fighting in conflicts abroad faced a jail sentence.
Hundreds of Saudis are believed to be fighting in Syria, and correspondents say Riyadh fears they could pose a security risk when they return home.
Although the kingdom has supported the Sunni-led rebels fighting to overthrow Syrian President Bashar al-Assad, it has long feared a backlash from radical jihadist groups.
Last month, King Abdullah decreed jail terms of up to 20 years for anyone belonging to “terrorist groups” or fighting abroad. The new law also promised tough sanctions for anyone backing the incriminated organisations.
However, rights group Amnesty International has criticised the legislation, saying it could be used to suppress peaceful political dissent.
Earlier this week, Saudi Arabia joined the United Arab Emirates and Bahrain in withdrawing its ambassadors from Qatar, which it sees as an important supporter of the Brotherhood.
The Muslim Brotherhood is already banned in Saudi Arabia, which has long viewed its ideology of populist Islam as a threat.
Analysts say the Brotherhood’s conservative Sunni doctrines are seen as a challenge to the Saudi principle of dynastic rule.
In Egypt, the Brotherhood has been driven underground since the army deposed President Mohammed Morsi, a longtime member of the group.
The military-backed government in Cairo designated the Brotherhood a terrorist group in December.