"Dialogue and military strategy (to combat terror) will continue...I do not agree that there is a lack of synchronisation between the two," Kerry told a joint news conference with National Security Advisor Sartaj Aziz after intensive meetings with Pakistan's top leadership.
Kerry refused to promise that US drone attacks inside Pakistan would stop and rejected the impression that the strikes were a violation of the country's sovereignty.
"And they attack people in mosques, (they) blow up people in villages, in market places, they are violating the sovereignty of the country."
Drone strikes have emerged as a key irritant in Pakistan-US ties, with Islamabad describing them as counter-productive.
More From This Section
Kerry said the US is gearing up for the drawdown of its forces in Afghanistan and to prepare the grounds for talks to organise the Afghan presidential election next year.
Troops of over Western 50 countries will remain to counter terrorism and help train Afghan forces, he said.
Kerry hoped the Afghan Taliban will return to negotiations as part of efforts to find a political solution to the Afghan problem.
"The reason we hope talks can take place is because everybody understands a political resolution is better than the continued fighting," he said.
As an apparent sop to Pakistan, Kerry announced that the US will resume the stalled strategic dialogue process in six months and also improve bilateral trade ties.