Security sources told MENA, the state news agency, that Aref was arrested in Nasr City in his father-in-law's home.
Hours after the arrest, photos of Aref in custody, smiling with the police forces that arrested him, spread on Egyptian news websites and on social media.
The last update posted by Ahmed Aref on his Facebook page was about how the January 25 Revolution was the last hope for Egypt against dictatorship.
"The only hope against oppression is the January 25 Revolution. We will not give up legitimacy and there is no place for military coups in front of people looking for freedom and dignity. May God protect Egypt, its people and its army," Aref said nine hours before his arrest.
Aref is the latest leading Muslim Brotherhood member to be arrested  in a campaign targeting leaders of the group across the country.
No official charges were announced following the arrest of Aref, who was reportedly transferred to Tora prison.