Friday's move appeared to enforce last month's royal decree where Riyadh said it would jail for between three and 20 years any citizen who fought guilty of fighting in conflicts abroad.
The kingdom's authorities want to deter Saudis from joining rebels in Syria and posing a security risk once they return home.
Riyadh also fears the Brotherhood, whose conservative Sunni doctrines challenge the Saudi principle of dynastic rule, has tried to build support inside the kingdom since the Arab Spring popular revolutions in the Arab-speaking world.
In Egypt, the Brotherhood, which won every election following the toppling of long-time ruler Hosni Mubarak in 2011, has been driven underground since the army deposed President Mohamed Mursi, a longtime member of the group that also endured repression in the Mubarak era.
The army-backed government in Cairo designated the Brotherhood as a terrorist group in December after accusing it of carrying out a suicide bomb attack on a police station that killed 16 people. The Brotherhood condemned that attack and denies using violence.
Saudi Arabia's Islamic religious authorities have previously spoken out against Saudi fighters going to Syria, but the Saudi Interior Ministry estimates that around 1,200 Saudis have gone there nonetheless.