The arrest of Essam el-Erian, the deputy leader of the Brotherhood's political arm the Freedom and Justice party, was the latest in a wide-ranging crackdown and prosecution of both the Islamist group's leaders and its rank-and-file since the removal of president Mohamed Morsi, who also hails from the Brotherhood.
Mr Morsi is in detention, held incommunicado at an undisclosed location and is due to appear in court on November 4 on charges of inciting followers to violence and murder.
Mr el-Erian was apprehended by security forces acting on a tip that led them to the apartment in the suburb of New Cairo.
The media-savvy Mr el-Erian was among few senior Brotherhood figures still on the run.
He was considered a more moderate leader but turned hardline and went into hiding after the popularly-backed coup that removed Mr Morsi, Egypt's first freely elected president.
Hundreds of Brotherhood figures have been arrested since the coup.