Speaking to reporters in Belgum, Kerry characterized the talks as a "continuing trilateral discussion" on looming security issues in Afghanistan and elsewhere in the region.
Washington, Kabul and Islamabad all face "a critical transformational period" in the months ahead of the U.S. withdrawal from Afghanistan, according to to Kerry.
"We’re very, very hopeful for a productive series of discussions," the State Department chief said.
Afghan President Hamid Karzai echoed those comments during the same Wednesday press conference, personally thanking Pakistani army chief Ashfaq Kayani and Foreign Secretary Jalil Jilani for participating in the talks.
In response, Jilani said Pakistan is committed to "moving forward to a very productive and forward-looking discussion" with his American and Afghan counterparts.
The talks come at a critical time in U.S.-Pakistan relations as the war in Afghanistan is coming to a close.
Tensions between Kabul and Islamabad hit a low point in March, when Pakistan withdrew from Afghan-led peace talks with the Taliban in Doha.
White House officials had hoped to fast-track Taliban peace plan, saying a deal would be "absolutely essential to bringing the war to a responsible close," Doug Lute, the administration's top adviser for South Asia, said in January.
But Islamabad's demand that Kabul cut all ties with Pakistan's long-time foe, India, as well as immediately sign a military cooperation pact with Pakistan was a clear sign that Islamabad was not ready to make a deal, Afghan officials said in March.
Islamabad's decision to back away from the talks is a huge blow to the Obama administration's postwar plans.
However, Gen. Joseph Dunford, head of all U.S. forces in Afghanistan, told Congress in April that Pakistan is not taking steps to sandbag the peace process, despite claims by Kabul.
"If we can bring that relationship together in a constructive way and establish a foundation of trust ... that can be the foundation of something deeper, some strategic partnership that would obviously take years to develop," he said.
Roughly 66,000 American troops remain in Afghanistan, with half of those forces scheduled to withdraw from the country this spring.
The final 32,000 American forces remaining in country will start coming home following the country's presidential election in April 2014 — officially ending America's combat role in Afghanistan.