A second bomb was defused.
The Arabic language daily al-Masry al-Youm said five people were injured, one critically, in the explosion outside Cairo's al-Azhar University.
A photo accompanying the report showed seats inside the bus covered with shattered glass.
Ahram Online described the blast as "a huge explosion. " Minister of Interior Alaa Abd el-Zahar told the website the bomb was thrown at the bus in front of the King Fahd School complex in the Nasr neighborhood adjacent to al-Azhar University and a police station. Zahar said security forces detonated a second bomb in the garden in front of the school. He said both bombs contained gunpowder, nails and marbles.
The Egyptian government Wednesday declared the Muslim Brotherhood a terrorist organization. In a statement to the press, Deputy Prime Minister Hossam Eissa said the decision was subject to Article 86 of the Egyptian penal code which defines terrorism and the penalties for engaging in it, Ahram Online said.
Eissa added Brotherhood members are suspected of involvement in the deadly bombing of police headquarters in Mansoura Tuesday that claimed 16 lives and also in attacks on churches and other violence, Ahram Online said.
The Brotherhood says it is not cowed by being branded a terrorist group by the military-led interim regime and will press on with opposition protests.
Cairo's declaration outlawing the Sunni Islamist religious, political and social movement and vowing to treat anyone who supports it as a terrorist, is a "worthless decision from an illegal gov't without any evidence and will not change anything in reality," the Brotherhood said on its official English-language Twitter page.
The Brotherhood's political Freedom and Justice Party said on Facebook the military's removal in July of Mohamed Morsi, Egypt's first democratically elected president and a former party leader, was "terrorism," not the Brotherhood's activities.
Hundreds of Brotherhood supporters took to the streets in towns and cities across Egypt after the regime's announcement Wednesday. Protesters in Alexandria, Egypt's second-largest city, threw improvised explosive devices at security personnel and set fire to police cars, CNN reported.
"The Muslim Brotherhood remains as it has been," the Cabinet of Prime Minister Hazem el-Beblawi said in a statement. "It only knows violence as a tool."