On April 13, 1904, Pinkham was appointed president of the territorial Board of Health. While president of the Board of Health, he developed the idea of dredging the marshlands of Waikīkī via a two-mile long drainage canal. Although the idea was approved by the Board of Health, no action was taken on the proposal. Over his two terms, Pinkham's achievements included improving the conditions of the lepers at the Molokai settlement, economically reducing the occurrence of bubonic plague and cholera in Hawaii. In 1907, Pinkham's remarks on the Japanese community's behavior during a bubonic plague outbreak were found to be offensive, and the Japanese community's reaction was a major factor in Governor Frear's decision to not reappoint Pinkham for another term. Pinkham was removed from the Board of Health on April 12, 1908.
In April 1909, Pinkham was employed as a labor commissioner by the Hawaiian Sugar Planters' Association to help transport Filipino labor recruits to Hawaii. After four years, the HSPA ended Pinkham's contract "because of differences of opinion about the methods and purposes of recruiting Filipino workers."
Despite having no previous political experience, U.S. President Woodrow Wilson appointed Pinkham territorial governor of Hawaii on November 29, 1913, succeeding Governor Walter Frear. His appointment was controversial among Hawaii Democrats. The U.S. Senate confirmed Pinkham's appointment by a vote of 46-24, by just one vote more than the two-thirds necessary for confirmation. Pinkham was the state's first governor from the Democratic Party, although his affiliations with the Republican Party were often under question. In 1917, during Pinkham's governorship, the deposed former monarch of the Hawaiian Islands, Queen Liliuokalani, died and was buried at the Royal Mausoleum of Hawaii. The construction of what would become the Ala Wai Canal and the drainage of the Waikīkī marshlands are credited for enabling the development of Waikīkī as a tourist center, and are considered to be one of the most enduring legacies of Pinkham's tenure. Pinkham also worked aggressively to improve the military defense of Hawaii. He voluntarily resigned from his position and was replaced by Charles J. McCarthy on June 22, 1918. Pinkham died November 2, 1922 in San Francisco, California.
