Prior to his judgeship, Baker was a legal advisor at the U.S. Department of State where he provided legal advice on law enforcement, intelligence, and counter-terrorism issues, and served as counsel to delegations to various environmental negotiations. He was the Deputy Legal Advisor to the National Security Council from 1994 to 1997, and Counsel to the President's Intelligence Advisory Board and Intelligence Oversight Board in 1993. From 1997 to 2000, he was a Special Assistant to President Bill Clinton and Legal Advisor to the National Security Council. At the NSC, Judge Baker advised the President, the National Security Advisor, and the National Security Council staff on national security law.
Baker is the recipient of the 1999 Colonel Nelson Drew Award, the NSC's highest honor, in recognition of his "distinguished contributions to the formation of peaceful, cooperative relationships between states, and U.S. security policy for global peace."
He is a recipient of the "Director's Award", given by the Director of Central Intelligence, in recognition of "superior contributions in the fields of intelligence and national security".