El-Erian, vice president of the Brotherhood's Freedom and Justice Party, faces charges that include inciting violence against Brotherhood opponents before President Mohamed Morsi was ousted, funding violent acts and thuggery, Ahram Online reported.
A warrant was issued against el-Erian in July.
During his time in hiding, el-Erian taped several video messages that were broadcast on al-Jazeera.
Ahram Online said the most pointed message was directed at the country's interim government leaders, described by el-Erian as "coup leaders," in which he demanded they recognize their "mistakes" and "confess that they've sided with one particular faction against another."
El-Erian was among the last few top Muslim Brotherhood members at large after most, including Morsi, were arrested.
The Brotherhood, which was registered as non-government organization after it was outlawed for years, was banned again in September.
A case to dissolve the Freedom and Justice Party is under review after the State Commissioners Authority recommended it be disbanded.
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