Karachi is Pakistan's economic hub, home to its stock exchange and a lifeline for a depressed economy wilting under inflation and stagnating foreign investment.
The southern port city is important to logistical support for the NATO forces fighting against Taliban militants in Afghanistan.
"We'll sit outside the port's gate from Saturday afternoon to Sunday evening continuously to block the trucks carrying NATO supplies," said cricket-hero-turned politician Khan, who leads Tehreek-e-Insaf (Movement for Justice).
"It will be our symbolic protest against the US atrocities towards our innocent citizens."
He had equally harsh words for President Asif Zardari's government and the main opposition leader Nawaz Sharif but refrained from passing similar comments about army chief Ashfaq Kayani.
Khan's party staged a two-day sit-in outside the northwestern city of Peshawar last month, which was called to urge the US to end a covert missile campaign against Islamist militants in Pakistan's tribal belt.
Khan said the government had given full liberty to its "American masters to kill Pakistanis at will."
"We'll be protesting against the drone strikes till our people are truly liberated from the clutches of monsters," he said.
NATO supply trucks and oil tankers are the targets of frequent attacks blamed on insurgents attempting to disrupt supplies for the more than 130,000 international troops fighting in Afghanistan.
Most supplies and equipment required by coalition troops in Afghanistan are shipped through Pakistan, although US troops increasingly use alternative routes through central Asia.