Kerry, who is visiting Afghanistan ahead of a trip to Pakistan to discuss strained bilateral ties, said Islamabad needed to improve efforts in fighting extremism, but the death of Bin Laden provided a critical chance to move forward.
"We obviously want a Pakistan that is prepared to respect the interests of Afghanistan, and to be a real ally in our efforts to combat terrorism," Kerry told reporters in the northern Afghan city of Mazar-i-Sharif.
"We believe there are things that can be done better. And there are serious questions that need to be answered in that relationship. But we're not trying to find a way to break the relationship apart; we're trying to find a way to build it."
US lawmakers have questioned whether Pakistan is serious about fighting militants in the region after Bin Laden was found living in Pakistan. Some have even called for a suspension in US aid to Islamabad.
Pakistan has rejected allegations the killing showed incompetence or complicity in hiding the al Qaeda leader.
Kerry, a Democrat close to the Obama administration and who is chairman of the Senate Foreign Relations Committee, said last week it was "extraordinarily hard to believe" Bin Laden could have survived in Pakistan for so long without any knowledge.
Current and former US officials, in private, say the United States repeatedly told Pakistan that Washington would send American forces into that country if it had evidence Bin Laden was hiding there.
Asked if the United States would conduct a similar raid inside Pakistan to kill Mullah Omar, the reclusive leader of the Afghan Taliban, if they knew his whereabouts, Kerry said Washington would consider all its options.
"The United States government will always reserve all of its options to be able to protect our people. Other plots have been conducted and organised and planned out of Pakistan. It is really critical that we talk with the Pakistanis as friends," Kerry said.
US officials have long maintained Omar fled to Pakistan after the Taliban government was overthrown in late 2001 by US-backed Afghan forces and is still in hiding there.
Islamabad has denied reports he is in Pakistan.
Kerry said Pakistan itself was a victim of extremism and faced its own tough decisions but that the killing of bin Laden provided a new opportunity.
"Sometimes those choices can be very difficult for people to make because of the pressures that they're under and the violence that occurs," he said.
"We respect and understand that, but this is the time, this is a critical time to find a better way forward and we hope that we're going to be able to do that."
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