Charles Edward Magoon (December 5, 1861 – January 14, 1920) was an American lawyer, judge, diplomat, and administrator who is best remembered as a governor of the Panama Canal Zone; he also served as Minister to Panama at the same time. He was Provisional Governor of Cuba during the American occupation of Cuba from 1906 to 1909.

He was the subject of several scandals during his career. As a legal advisor working for the United States Department of War, he drafted recommendations and reports that were used by Congress and the executive branch in governing the United States' new territories following the Spanish–American War. These reports were collected as a published book in 1902, then considered the seminal work on the subject. During his time as a governor, Magoon worked to put these recommendations into practice. In summary: Magoon was hugely successful in Panama but criticized for his tenure in Cuba.

Magoon was born in Owatonna, Minnesota. His family moved with him to Nebraska when he was still a small child. In 1876, he enrolled in the "prep" program at the University of Nebraska and studied there for two years before officially enrolling in 1878. He left school in 1879 to study law independently with a prominent law firm. In 1882, he was admitted to the bar and practiced law in Lincoln, Nebraska. Eventually, he was made a partner in the firm. He also became the judge advocate of the Nebraska National Guard and continued to use the title of "Judge" throughout the remainder of his career.

By 1899, Magoon was sought out to join the law office of the newly created Division of Customs and Insular Affairs, later renamed the Bureau of Insular Affairs, in the U.S. Department of War under Secretary of War Russell A. Alger.

Legal and political controversies had arisen regarding whether the people of the newly acquired territories were automatically granted the same rights under the United States Constitution as American citizens. Magoon prepared a report to Alger in May 1899 that would have established the official departmental policy as "the Constitution follows the flag."

Under this view, the moment the treaty transferring the territories to U.S. sovereignty was signed, the residents of Puerto Rico, the Philippines, and other territories became subject to all the rights granted by the Constitution. For the new territories following the Spanish–American War, this would have been from the signing of the Treaty of Paris on December 10, 1898. With the resignation of Secretary Alger, this incomplete report was not released to Congress.

In August 1899, Elihu Root became the new secretary of war, and the unreleased report was scrapped. Magoon drafted a new report which came to precisely the opposite conclusion from the first: the Constitution did not apply in new territories until the United States Congress specifically passed legislation to authorize it. It argued that precedent was set when Congress passed legislation to apply the Constitution to the Northwest Territory and the Louisiana Purchase. This revised report was dated February 12, 1900, and released to Congress as a policy document expressing the Department's official stance on the issue. This view was largely adopted by the Supreme Court of the United States beginning in 1901 in the so-called "Insular Cases."

During this period, Congress was debating a Puerto Rico Tariff Act that would have been unconstitutional had the first definition been kept. This was a largely partisan issue at the time—the Republicans were in favor of this Act, but it was strongly denounced by Democrats. During the ensuing debate, the existence of the original report was discovered by the Democrats, who requested that the War Department release the earlier report to them so they could be compared "side by side". The request was refused, but a copy of the report was leaked, allowing Minority Leader James D. Richardson to read it aloud on the Senate floor, prior to the vote. These efforts failed; the vote remained along party lines and the measure was passed.