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APU, chartered as Alaska Methodist University by the Territory of Alaska in 1957, dedicated its campus on June 28, 1959, the same year Alaska achieved statehood. When the first students enrolled in classes beginning October 1, 1960, campus facilities consisted of Grant Hall, the academic and student center; and Gould Hall, the student residence. As enrollments and programs grew significantly, a student center, apartment and residence hall complex was constructed. This complex was later named Atwood Center.

After a 1977 reorganization, academic programs were restructured, and in November 1978, Alaska Methodist University was renamed Alaska Pacific University to better reflect its educational mission and geographical location.

The Ruth and Homer Moseley Sports Center was added to campus facilities in 1986 and the Carr Gottstein Academic Center in 1992. The university now offers eleven undergraduate majors and five graduate programs.