Immediately following graduation from FSU in 1994, Cooper joined the Washington, D.C. legislative staff of Florida Republican Congresswoman Ileana Ros-Lehtinen.

While Aide to Davidson, Cooper was known for actively advocating for the protection of archeological sites and artifacts, particularly the ancient city of Babylon.

[citation needed] In 2001, Cooper joined the ranks of Bush appointees as an assistant director of the National Park Service, where he advocated for greater access to public lands and was part of Interior Secretary Gale Norton's efforts to challenge Clinton administration executive orders restricting use and access of public lands.

During the second term, Cooper served several diplomatic postings including United States Embassy in Baghdad, where as an advisor to Ambassador Zalmay Khalilzad, often travelled with members of Congress in the Middle East region.

During his tenure, he implemented reforms to streamline arms export licensing and improve government support to American defense industry.

[11][12][13] At Cooper's 2019 ceremonial swearing-in on the 230th anniversary celebration of the founding of the State Department, Secretary of State Mike Pompeo noted, “…with his two decades of experience in both military and diplomatic roles, I'm confident that Clarke is the right person for the job.”[14] Among enabling bilateral security partnerships, and advocacy for burden sharing to counter shared threats, Cooper was also known for his longtime advocacy of performance measures across UN peacekeeping missions, women in active peacekeeping roles, and accountability measures for troop and police contributing countries.

[27][28] At the time, former Governor Jeb Bush noted, "During my administration, Clarke was part of an excellent team that built improved relations with the federal government that benefited the citizens of Florida.

[33] In 2013, Cooper was the featured conservative in Timothy Greenfield-Sanders' HBO Documentary "The Out List," and was among notable Republicans who were signatory to an amicus curiae brief submitted to the United States Supreme Court in support of same-sex marriage during the Hollingsworth v. Perry case.