Baer was raised in Aspen, Colorado and aspired to become a professional skier. After a poor academic performance during his freshman year at high school, his mother sent him to Indiana's Culver Military Academy. In 1976, after graduating from the Georgetown University School of Foreign Service and entering the University of California, Berkeley, Baer decided to join the CIA's Directorate of Operations (DO) as a case officer. Upon admittance to the CIA, Baer engaged in a year's training, which included a four-month paramilitary course.

During his twenty year CIA career, Baer has publicly acknowledged field assignments in Madras and New Delhi, India; in Beirut, Lebanon; in Dushanbe, Tajikistan; and in Salah al-Din in Kurdish northern Iraq. While in Salah al-Din Baer unsuccessfully urged the Clinton Administration to back an internal Iraqi attempt to overthrow Saddam Hussein (organized by a group of Sunni military officers, the Iraqi National Congress' Ahmad Chalabi, and the Patriotic Union of Kurdistan's Jalal Talabani) in March of 1995 with covert CIA assistance. Baer quit the Agency in 1997 and received the CIA's Career Intelligence Medal on March 11, 1998. Baer wrote the book See No Evil documenting his experiences while working for the Agency.