Prosecutors have ordered the detention of Essam El-Erian for 30 days pending investigations into charges of instigating street clashes.
The vice president of the Muslim Brotherhood's Freedom and Justice Party will be held for 15 days over clashes between local residents and supporters of Mohamed Morsi in Giza's Bayn Al-Sarayat district in July, and for 15 days over clashes near Giza's Al-Istiqama Mosque in August.
He denies the charges.
Security forces arrested El-Erian at a flat in Cairo’s Fifth Settlement suburb in the early hours of Wednesday after receiving a tip off.
Pictures of the arrest, published on the interior ministry’s social networking pages, show El-Erian smiling to the cameras.
During his time in hiding, he pre-recorded a number of video messages that were broadcast on Al Jazeera.
The most notable of these messages was directed at the country’s interim government or what El-Erian described as ‘coup leaders’, demanding they recognise their "mistakes" and “confess that they’ve sided with one particular faction against another.”
In September, he was charged in absentia for his alleged involvement in clashes in Giza's Al-Bahr Al-Azam district in July.
He also faces separate charges of inciting the murder of protesters on several other occasions, including at the Ittihadiya presidential palace in December 2012 and at the Brotherhood headquarters in June 2013. A number of other Brotherhood leaders are being investigated on the same charges.
El-Erian was one of the few high-ranking Brotherhood members to remain at large after most, including Mohamed Morsi, had been arrested.
The Brotherhood, which was registered as an NGO, was banned on 23 September.
A case to dissolve the FJP is currently being reviewed after the State Commissioners Authority, a body that provides non-binding legal advice, recommended its disbandment.