"We're at a pivotal period," the official said. "These type of negotiations are, of course, complex, whether it's technical issues or tough security issues."
Lack of immunity for U.S. troops was a crucial factor in the failed attempt to set up a postwar security deal in Iraq, and it set the stage for the recent wave of sectarian violence against Iraqi forces and civilians in the country.
While President Obama has been adamant that an agreement is critical to American postwar plans in Afghanistan, Kerry's visit comes at an important time for U.S -Afghan relations.
With the final American combat units set to pull out of the country next year, both countries are still no closer to reaching an agreement to allow a small contingent of American and allied forces in Afghanistan after the 2014 withdrawal.
"Both President Karzai and Secretary Kerry agreed that a visit would be helpful, not just for the sake of a visit but to discuss some of the issues of mutual concern," a second State Department official added.
Most recently, Washington's plan to have U.S. special operations forces and American intelligence operatives conduct missions against the Taliban and al Qaeda elements inside Afghanistan after the White House's 2014 withdrawal deadline is "a deal breaker," according to Aimal Faizi, spokesman for Karzai.
Underlying tensions recently hit a boiling point Monday, when Karzai said his country is willing to walk away from postwar talks with the United States if Washington does not comply with his demands.
"If it doesn't suit us, and if it doesn't suit them then, naturally we will go separate ways," he said in an interview with the BBC.
"If this agreement does not provide Afghanistan peace and security the Afghans will not want it," Karzai added.
Additionally, Karzai claimed the 12-year war in Afghanistan has done nothing to improve the country's security.
The Afghan war, which officially entered its 13th year Monday, "was one that caused Afghanistan a lot of suffering, a lot of loss of life, and no gains because the country is not secure," according to Karzai.
"What we wanted was absolute security and a clear-cut war against terrorism," Karzai said at the time.
NATO Secretary General Anders Fogh Rasmussen fired back sharply against those claims Thursday.
“Thanks to the immense efforts and the solemn sacrifices of the troops and civilians from [NATO] ... Afghanistan has come a long way in the past decade,” Rasmussen told reporters at alliance headquarters in Brussels.
“The changes have been remarkable, and our investment in lives and resources has been unprecedented. Nobody can deny that. And this effort should be respected," he added.
Despite those growing tensions, American officials remain adamant that a BSA will be in place by the end of the year.
"The goal here was to complete the BSA in October [and] . . . we continue to believe that that is both preferable and doable," the second department official added.
There are roughly 55,000 U.S. troops in Afghanistan, but most are expected to go back to the United States over the coming months.
The final American units will return stateside after the April 2014 presidential election, marking the end of the American war in Afghanistan.
--This story was updated at 3:11pm