In a statement on Friday, the group said that the security forces had arrested its deputy head Zaki Bani Rsheid on Thursday, Xinhua reported.
"We are surprised by the arrest of Bani Rsheid and call for his release," said the statement.
Bani Rsheid was arrested after he published an article that the authorities considered harmful to Jordan's relationship with the United Arab Emirates (UAE).
In his article, Bani Rsheid had criticised the UAE for designating the Islamist organisation as a terrorist group.
Jordan's Muslim Brotherhood is the country's biggest opposition party.
Bani Rsheid is the third senior Brotherhood figure to be arrested in recent months in Jordan.