Khayrat el-Shater, the Brotherhood's No 3 member and a leading strategist, was among 29 others whose assets were ordered frozen late January by an Egyptian prosecutor.
He was arrested in mid-December along with about 140 other members on allegations they were recruiting students and providing them with combat training, knives and chains.
The last time a group of Muslim Brotherhood members was referred to a military court was in late 2001, when 22 were put on trial, a lawyer for the group, Abdel-Moneim Abdel-Maksoud said.
The banned organisation is Egypt's largest political opposition group and won 88 of parliament's 454 seats in 2005 elections, with its candidates running as independents.
The group, founded in 1928, was banned in 1954.