Schroen worked with the Agency for over 30 years, rising from case officer to Deputy Chief, Near East Division, Directorate of Operations in 1999, a post he held through 2001. During his career, Schroen served in numerous posts, including Station Chief in Kabul, Afghanistan (but working out of Pakistan) in the late 1980s. From 1992-1994, Schroen worked at CIA headquarters in Langley, Virginia, controlling Iranian operations. Schroen was the chief of station in Islamabad, Pakistan from 1996 until mid-1999. During this period, he directed CIA operations to find and capture Osama bin Laden, and began renewing relationships with the Mujahideen commanders who fought the Soviets in the Soviet-Afghan War.
Although he planned to retire, Schroen was recalled after the September 11th attacks to lead a CIA team into Afghanistan. The seven-officer team, which included renowned covert operativeBilly Waugh, flew into Afghanistan on September 26, and began securing support among the Northern Alliance shortly before the arrival of US Army Special Forces ODA 555. He has since written the book First In, illustrating his Afghan experiences. Schroen was one of several inspirations for The Path to 9/11 character CIA Operative "Kirk", who writers claimed was a compilation based on several actual people.