PESHAWAR, Pakistan — The Pakistani military said Saturday that it had killed a senior leader of Al Qaeda wanted in the United States on charges of plotting to bomb several Western targets, including the New York City subway system.

The death of Adnan G. el-Shukrijumah, described by the F.B.I. as a leader in Al Qaeda’s external operations program, marks a major counterterrorism victory for the Pakistani military, and is likely to further improve fraught relations with the United States.

Mr. Shukrijumah was killed either late Friday or early Saturday in a raid at a remote compound in the tribal district of South Waziristan, which is home to many militants and is a major focus of the C.I.A.-led drone campaign. It comes just over a week after a trip to Washington by the Pakistani Army chief, Gen. Raheel Sharif, who met with Secretary of State John Kerry and American military leaders in a visit intended to repair a strategic relationship that has long been scarred by acrimony and mistrust.

Mr. Shukrijumah, 39, a naturalized American citizen who was born in Saudi Arabia, was indicted in the United States in 2010 for what prosecutors say was his role in a plot, uncovered the previous year, to bomb the New York subways. The F.B.I. had offered a $5 million reward for information leading to his capture.