The Tuesday decision by the administrative court was expected. Government officials have called the broadcasts of Al-Jazeera Mubasher Misr a national threat, saying it operated without a permit and accusing it of spreading rumors.
The station extensively covered Brotherhood protests following the July 3 military coup that toppled Islamist President Mohammed Morsi, who hails from the Islamist group, after millions took to the streets demanding his ouster.
Egyptian officials and media say the station is biased toward the Brotherhood, a charge Al-Jazeera denies.
The other three stations, considered pro-Islamist, have also covered Morsi protests.