The game was initially set to be played away from home but it was played in Cairo after the Zanzibar side accepted to play the two legs in Cairo.
Congolese striker Fiston Mayele needed only nine minutes to open the scoring for the Egyptian side with a close-range header.
Six minutes later Moroccan midfielder Walid El-Karti doubled the lead with another header.
Midfielder Mohanad Lashin added the third in the 26 th minute with a nice shot from outside the area, while winger Ibrahim Adel made it 4-0 after seven minutes.
The second half saw Mohanad Lashin score another goal to register a rare double in the 55 th minute.
Winger Mahmoud Abdel-Hafiz completed the rout, two minutes from time, as the Egyptian representative put one foot in the next round.
Pyramids FC will host JKU in the second leg on Saturday at the same stadium in Cairo.
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