In a speech celebrating the birthday of the Prophet Muḥammad, which coincided with New Year's Day, he said they had no time to lose.
"I say and repeat, again, that we are in need of a religious revolution. You imams are responsible before Allah. The entire world is waiting on you. The entire world is waiting for your word ... because the Islamic world is being torn, it is being destroyed, it is being lost. And it is being lost by our own hands," el-Sisi said.
"We need a revolution of the self, a revolution of consciousness and ethics to rebuild the Egyptian person -- a person that our country will need in the near future," the President said.
El-Sisi, himself a pious man, was elected in May after leaving the military to run for the office.
A former defense minister, he led the ouster of Mohamed Morsy -- the Islamist who was Egypt's first democratically elected President -- and has long positioned himself as a more secular option, and defender against extremist views.
"It's inconceivable that the thinking that we hold most sacred should cause the entire Islamic world to be a source of anxiety, danger, killing and destruction for the rest of the world. Impossible that this thinking -- and I am not saying the religion -- I am saying this thinking," el-Sisi said.
He continued: "This is antagonizing the entire world. It's antagonizing the entire world! Does this mean that 1.6 billion people (Muslims) should want to kill the rest of the world's inhabitants -- that is 7 billion -- so that they themselves may live? Impossible!"
While el-Sisi's speech included some powerful language, H.A. Hellyer, a nonresident fellow at the Center for Middle East Policy at the Brookings Institution and research associate at the Kennedy School of Government at Harvard University, said the President has made similar statements in the past.
"There is little to suggest (el-Sisi) is interested in some sort of Lutheran reformation of Islam. By all accounts, he's quite comfortable with the prevailing leadership of the Azhari establishment.
"If anything, he wants to empower it further in order to push forward a counternarrative against radical Islamism. The real question is: How credible can such a state-empowered counternarrative be?" Hellyer said.
On Tuesday, the President visited the main Coptic cathedral in Cairo to attend a Christmas mass and make a short speech. He is the first president to attend such a mass since the revolution.
"We will build our country together. We will accommodate each other. We will love each other," el-Sisi said in that speech.