"Shame, shame on the U.K.," protesters chanted.
They called for Gibbons' execution, saying, "No tolerance: Execution," and "Kill her, kill her by firing squad."
The women's prison where Gibbons is being held is far from the site. Unity High School, which is closer by in central Khartoum, is under heavy security protection.
The protest arose despite vows by Sudanese security officials the day before, during Gibbons' trial, that threatened demonstrations after Friday prayers would not take place. Some of the protesters carried green banners with the name of the Society for Support of the Prophet Muhammad, a previously unknown group.
Many protesters carried clubs, knives and axes - but not automatic weapons, which some have brandished at past government-condoned demonstrations. That suggested Friday's rally was not organized by the government.
A Muslim cleric at Khartoum's main Martyrs Mosque denounced Gibbons during one sermon, saying she intentionally insulted Islam. He did not call for protests, however.
"Imprisoning this lady does not satisfy the thirst of Muslims in Sudan. But we welcome imprisonment and expulsion," the cleric, Abdul-Jalil Nazeer al-Karouri, a well-known hard-liner, told worshippers.
"This an arrogant woman who came to our country, cashing her salary in dollars, teaching our children hatred of our Prophet Muhammad," he said.
