Karzai has hedged on when he will sign the deal despite a four-day "loya jirga" assembly of 2,500 tribal elders and politicians endorsing it and urging him to sign it promptly.
Opening the assembly in Kabul on Thursday, Karzai exasperated Washington by saying he wanted to delay signing the deal until after the successful completion of April's presidential election.
The bilateral security agreement (BSA) will permit some US soldiers to remain after the end of 2014 when most of NATO's 75,000 troops pull out.
US national security adviser Susan Rice's trip to Afghanistan, which began on Saturday but was kept under wraps, was "long-planned", an official said.
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But the meeting with Karzai was added to Rice's itinerary at his request, National Security Council spokesman Patrick Ventrell told AFP.
The US embassy in Kabul said the meeting would take place tonight.
Karzai said yesterday he would "continue bargaining" on the BSA, which was hammered out just in time for the jirga after months of difficult negotiations with Washington.
US Secretary of State John Kerry said the assembly's vote was a "compelling affirmation from the Afghan people themselves of their commitment to a long-term partnership with the United States".
"Very significantly, the loya jirga also urged that the Bilateral Security Agreement (BSA) should be signed before the end of the year," he said.
The Taliban, who before the assembly had threatened to target delegates if they backed the agreement, condemned the pact.
After four days of discussions under tight security, jirga delegates anxious to conclude the deal with Afghanistan's main financial and military partner said in their closing statement that Karzai should sign before the end of 2013.
Karzai also appeared to toughen his stance on US military raids on Afghan homes, a sensitive topic that threatened to derail the deal last week.