The 26-year-old injured his knee during a league game against al-Ittihad on Thursday.
El-Shenawy had played a key role in Egypt's World CUp qualifying campaign, which saw the Pharoahs secure a place in the competition for the first time in over 20 years.
His injury means that Egypt will likely field veteran keeper Essam el-Hadary at the competition in Russia. At 45, El-Hadary would become the oldest player to feature in the games.
Posting on Twitter, El-Shenawy gracefully accepted the situation, asking his fans and supporters to pray for his recovery.
"I want to thank Allah for everything, this is my fate and I accept it," El-Shanawy said.
"This injury is a test from Allah, the anterior cruciate ligament injury was confirmed and I will travel to Germany soon for treatment. I need a prayer from all of you," he added.