As a Coast GuardLieutenant, Skinner commanded the USCGC Sea Cloud, a weather ship. When the United States entered World War II, the Coast Guard was integrated into the Navy, and the Sea Cloud was sent out on combat service. Leaving Boston, the Sea Cloud participated in sinking one submarine. Earlier, while serving as executive officer of the USCGC Northland, Skinner began to question the Armed Forces policy of ship segregation. The Northland, stranded during a patrol with no engine, was saved when a black steward crewman got the engine started after white engineers were unable. When Skinner recommended the man for promotion, he was told that blacks were only allowed to be steward's mates. Seeking to prove a point, Skinner sailed with the Navy's first fully integrated crew since the Civil War, with duties spread equally among white and black crewmen. Nationally renowned black artist Jacob Lawrence, whose paintings were already in the collections of New York's Museum of Modern Art and the Phillips Collection in Washington, D.C., was among the men who served on the Sea Cloud under Lieutenant Skinner. After the Sea Cloud, Skinner commanded a second integrated crew aboard the USS Hoaquim near the Aleutian Islands. Noting the success of Skinner's two commands, the Navy integrated the USS Mason, and dropped ship segregation completely within the next few decades. Master Chief Petty Officer of the Coast Guard Vincent W. Patton III said of Skinner: "I will say without question that he was the front guard of integrating the U.S. military forces in World War II, and the man got very little credit for it".
Governorship
When the Department of the Interior began to oversee Guam, Skinner was a Public Relations Officer for the Department. After the Department selected him and the Department of the Navy ceded control, Truman appointed Carlton Skinner governor of Guam on September 17, 1949. As governor, Skinner established Guam's first university at the University of Guam. He also wrote the Constitution of Guam, which is still in use today.
A plaza in Agana is named in Skinner's honor. Tilton School Skinner and his wife, Solange P. Skinner, had a deep relationship with his alma mater, Tilton School. They often visited the campus, gave advice to the administration concerning the school's climate, and were major donors to the school. They created The Governor Carlton Skinner and Solange Skinner Fellowship at Tilton School, to “provide financial assistance to a student or students who exhibit a consistent sense of personal integrity, loyalty, and curiosity and who have demonstrated a commitment to fight injustice in all its forms.” Skinner was awarded the George L. Plimpton Award from Tilton in 1989 for his "passion for equality and freedom". Tilton School named part of their new academic building Skinner Tower, a 2-story glass tower which connects Plimpton Hall to the new academic building. In addition, The Governor Carlton Skinner Prize is "awarded annually to a member of the graduating class who, in the opinion of the Student Assembly and the Head of School, has consistently demonstrated a sense of personal integrity, loyalty, curiosity, and who has demonstrated a commitment to fight injustice in all its forms."