Demonstrators demanded that the Pakistani government sever ties with the U.S. over the raid that killed the al Qaeda leader.
A hard-line group with suspected militant ties organized the rally.
Speaking in Afghanistan, Massachusetts Sen. John Kerry took aim at Pakistan's government saying its relationship with the U.S. is at a critical juncture.
Kerry, who was on his way to Pakistan, also addressed growing suspicion that Pakistan's security forces were complicit in harboring bin Laden.
"There is some evidence of Pakistan government knowledge of some of these activities in ways that is very disturbing," Kerry said. "That will be without any question one of the subjects of conversation, it will not be a first time that conversation has been had with officials in Pakistan."
Kerry is the chairman of the senate Foreign Relations Committee and the most senior American official to travel to Pakistan since the raid on bin Laden's compound.
Seemingly supporting Kerry's claim, Afghanistan's former intelligence chief said in an interview he knew bin Laden was hiding in Pakistan four years ago, but Pakistan's leaders rejected his information.
In an interview broadcast Sunday on CBS' "60 Minutes," Amrullah Saleh said Afghan intelligence thought bin Laden was in the Pakistani city of Mansehra - about 12 miles away from Abbottabad, where the terrorist leader was eventually found and killed by U.S. Navy SEALs.
Saleh has become a prominent critic of Afghan President Hamid Karzai's efforts to start peace talks with the Taliban. He says Pakistan should be recognized by the U.S. as "a hostile country."
He told CBS: "They take your money. They do not co-operate. They created the Taliban. They are number one in nuclear proliferation."
The Associated Press contributed to this report.