The 60-year-old shopkeeper, identified as Magdy Habashi, was abducted on Saturday in the city of Sheikh Zweid. His remains were found in a cemetery on Thursday, according to news agencies.
A Coptic Christian priest, Mina Abboud Sharobeen, was shot dead by gunmen on July 6 in al-Arish city in northern Sinai.
Investigators suspect Islamist extremists are behind the two murders.
Egypt's Christians make up around 10 percent of the country's population and have frequently been targeted by Islamists.
In May, extremists shot dead a 28-year-old man who ran a bar in al-Arish.