In 1903, the school was 'reborn' and re-incorporated as a different entity, different trustees, and a different name: the 'University of Puget Sound'. It opened up a year later (1899) back in Tacoma on the 9th and G Street. It moved locations three times in 13 years and, at one time, the school was merged with Portland University (former campus is now the University of Portland).

There was no endowment and the school often struggled for funds to pay the professors. The university also had a financially tumultuous beginning. The beginnings of the school were marked by moral conviction: students were warned against intoxicating liquors, visits to saloons, gambling, tobacco use, and obscene drawings or writings on the college grounds. In September 1890, UPS opened its doors, taking in 88 students. At this time, the school's legal title was 'The Puget Sound University'. This date marks the legal beginning of the school. A charter was drawn up and filed in Olympia on March 17, 1888. The committee eventually decided on Tacoma. Two cities vied for the location of the school: Port Townsend and Tacoma. and so by united and prayerful efforts advance to the establishment of a school of learning which shall be a praise in all the land. command the respect and patronage of Methodist people within the bounds of the territory. heartily to the building up within the bounds of the conference of an institution of learning which shall by its ample facilities. Fowler was in Tacoma for a Methodist conference when he spoke of his vision of a Christian institution of learning in the area. The idea for a college in Tacoma originated with Charles Henry Fowler, who had previously been the president of Northwestern University. The University of Puget Sound was founded by the Methodist Episcopal Church in 1888 in downtown Tacoma.

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