Gamal and Alaa Mubarak were put on trial following the 2011 ousting of the late president, who ruled Egypt for 30 years. They have since been acquitted of all charges.
The asset freeze decision also included Gamal Mubarak’s wife Khadiga El-Gammal and his children Mahmoud and Farida.
The decision to freeze the assets was issued in 2012 over accusations of manipulating the stock exchange.
The economic court’s ruling on Tuesday is unappealable.