The unnamed student who studies commerce at the Suez Canal University in Ismailia, was arrested after the university's administration filed a complaint over his alleged activities, Egypt's largest news organisation Al-Ahram online writes.
The newspaper adds the accused student is now being investigated by national security officials.
While the story has yet to be verified by other sources, article 98 of Egypt's penal code says anyone found guilty of offending religion in any form can face up to six years in prison.
In December last year, a Cairo court convicted Coptic Christian blogger Alber Saber of blasphemy and contempt of religion, sentencing him to three years in prison.
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Saber had shared the anti-Islam film Innocence of Muslims, which portrays the Prophet Muhammad as a fraud, womaniser and buffoon, on social networking sites.
Saber's arrest was viewed by several rights advocates as a campaign led by Egypt's ultraconservative Islamists to curb free expression. He was later released after paying bail.
Atheism is on the rise in the country, with one non-believer telling the Egypt Independent he estimates the number to be around 3million.
Speaking in September, Othman Otham also revealed atheists do not label themselves as thus as society would "disown them".
Christians make up about 10 percent of Egypt's population of 85 million.