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Sheldon Jackson College is the oldest educational institution in continuous existence in the State of Alaska. It had its beginning in 1878 when Presbyterian missionaries John G. Brady (later Governor of Alaska) and Fannie Kellogg opened the upper floor of an old military barracks as a training school for Tlingit Indians. In 1882, the building burned to the ground. Another Presbyterian missionary, Dr. Sheldon Jackson, came to the rescue. He initiated a nationwide fund-raising campaign, and later that year a new building was constructed on the site of the present campus. Dr. Jackson was later named Alaska's first General Superintendent for Education.

By 1884, the school was known as the Sitka Industrial and Training School. A few years later, it became an elementary school. In 1910, the year of Dr. Jackson's death, the school was renamed Sheldon Jackson School. In 1917, a new boarding high school was added.

The college program was organized in 1944 as an extension of the high school curriculum; and in 1966, the year before the high school closed, Sheldon Jackson was accredited.

In 1972, the Presbyterian Church relinquished its direct authority for the operation of Sheldon Jackson College, ending the institution's 93 years of ownership by the Board of National Missions of the United Presbyterian Church in the U.S.A. The college is now owned and operated by an independent board of trustees. The college continues to preserve and honor its Christian heritage by maintaining covenant relationships with the Presbyterian Church (U.S.A.) and with the Alaska/Northwest Synod.

The college has grown into a four-year institution offering associate and bachelor degrees to students from widely diverse backgrounds. Emphasis on providing students with a broad-based, liberal arts education has increased.