The Woodland Park Zoo began its existence as a small private animal collection established by Seattle developer Guy C. Phinney (1852-1893) on the northwest corner of his 179-acre Woodland Park Estate. This menagerie included North American animals like deer and black bear, as well as more exotic specimens like African ostriches. After Phinney's death in 1893, the property remained in limbo until the City purchased it from Phinney's widow in 1899 for $100,000, despite a veto by Mayor Thomas D. Humes. It became a part of the municipal parks system and was overseen by the Department of Parks and Recreation. The menagerie grew in 1903, when the animals from a private zoo in Leschi Park were absorbed, providing the foundation from which Woodland Park Zoo would grow.

The zoo developed gradually during its first half-century. New facilities like the Lion House (completed 1919) and the Beaver Pool (completed 1936) were periodically opened and populated with new specimens brought in from around the world. Controversy arose in 1932 when, against fierce public opposition, the city went forward with plans to construct a six-lane highway (now Aurora Avenue) directly through Woodland Park, separating the zoo from the larger lower park area to the east. Historical events affected the zoo's operation, as with slashed budgets and near closure during the Great Depression, and an anti-aircraft gun emplacement in the North Meadow during World War II.

The postwar period featured more rapid expansion as well as a growing incorporation into municipal society. Buoyed by municipal bond issues in 1948 ($800,000) and 1960 ($150,000), the zoo completed a diverse set of new facilities, including an Animal Health Department (completed 1953) and the Great Ape House (completed 1957). A longtime inhabitant of the latter building was a male lowland gorilla named Bobo, who was the zoo's most famous resident from 1953 until his death in 1968. The zoo's profile was raised further in 1954 by the new KCTS children's program "Buttons and his Buddies," which followed zoo animals and staff during its 17-year run on the air. The most consequential development of this time, ultimately, may have been the 1965 founding of the Seattle Zoological Society (later Woodland Park Zoological Society) as a promotional and fund-raising organization auxiliary to the Parks Department.

The zoo received a significant financial boost in 1968, when the Forward Thrust program earmarked $4 million for a program of facility building and improvement at Woodland Park. The City enlisted a team led by architect George Bartholick to construct a long-range design plan. The Bartholick Plan, as it was known, envisioned a zoo of larger and more naturalistic exhibit spaces, but also - and more controversially - a connection to the lower park via a lid over Aurora Avenue. Concerned over the potential effect on existing park space, a citizen coalition called Save Woodland Park led a movement in opposition that resulted in the plan's 1974 defeat by public vote. Mayor Wes Uhlman then empanelled a task force of citizens and experts to formulate a new strategy, which eventually resulted in the Hancocks/Jones & Jones Plan, approved in 1976. Though less ambitious than the Bartholick Plan, the Long-Range Plan still incorporated naturalistic elements in the form of ecology-based "bioclimatic zones" into the design, setting a conceptual benchmark for future development.

Guided by the Long-Range Plan as well as growing public interest in issues of zoological conservation, Woodland Park Zoo subsequently committed to creating facilities that closely resembled the natural habitats of their animals. For example, 1979 saw the opening of the Lowland Gorilla exhibit, one of the first in the world to exchange generic cage space for native flora and landscaping for large primates. Following the exhaustion of Forward Thrust funds in the early 1980s, the zoo entered a period of financial stagnation, partially alleviated by donations and admission fees (first charged in 1977). Public concern in 1984 prompted Mayor Charles Royer to empanel a Zoo Commission of citizens, staff, labor representatives and civic leaders to consider the problem. The report published the following year recommended a new round of county bond issues for needed capital improvements. Passed by voters that November, the bonds generated $31.5 million, along with $10 million in private matching donations, and resulted in facilities like the Asian Elephant Forest exhibit (completed 1989).

New funding concerns prompted the creation of the Zoo Commission II in 1995 to formulate a fresh round of recommendations. In its report, the commission criticized the zoo's managerial organization, which split tasks between the City's Department of Parks and Recreation and the private Woodland Park Zoological Society, as cumbersome and wasteful of money and effort. In response, the City Council voted in 2001 to consolidate zoo administration under the Society. Under the terms of the 20-year contract signed in 2002, the Society was designated to take over full management of the zoo. The City oversees the contract and provides annual public funding. Today the zoo maintains a reputation for excellence among U.S. zoos for exhibits and education programs, and its 1,100 animal specimens attract over a million visitors per year.