Shukrijumah was believed to have been the former external operations chief of the Islamist terrorist network.
The FBI had offered a $5m reward for the capture of the Saudi national over a plot to target the New York subway, described by prosecutors as the most serious threat to the city since the 9/11 attacks.
The Pakistani military said Shukrijumah was shot dead in a raid on an al-Qaeda hideout in Shinwarsak, in the remote border region of South Waziristan, early on Saturday morning.
Two other militants died and five were arrested during the raid, the military said. One Pakistani soldier was killed and another wounded.
The military said that Shukrijumah had recently been forced to move by a Pakistani military operation in neighbouring North Waziristan.
The region was the Taliban’s key stronghold in Pakistan and a hotbed of militancy until the military launched an offensive to retake the territory on June 15.
An intelligence official said that security forces had been investigating reports that Chinese hostages were being held in Shinwarsak. Pakistani forces then learned about the presence of Shukrijumah and cordoned off the area, the officer said.
Two intelligence officers said the militants opened fire on the Pakistani military and Shukrijumah, who one described as “an Arab national,” was killed in the ensuing gun battle.
Shukrijumah, a Saudi Arabian native with a Guyanese passport, is wanted in the United States for conspiracy to use weapons of mass destruction and to commit murder in a foreign country.
According to the FBI website: “The charges reveal that the plot against New York City’s subway system, uncovered in September of 2009, was directed by senior al-Qaeda leadership in Pakistan.”
The subway plot was described by prosecutors at the time as described as the most serious threat to New York since the September 11, 2001 attacks.
Shukrijumah was also linked by US authorities to other terror suspects, including a cell accused of planning to bomb fuel pipelines at New York’s John F. Kennedy International Airport.