The Zoo opened in the Springfield section of Jacksonville on May 12, 1914 with an animal collection that started with one red deer fawn.

Several domestic animals were added later and a "monkey island" was established. On July 19, 1925, the Municipal Zoo, as it was then known, opened at its present site bordering on the Trout River. Starting with 37.5 acres, the Zoo continued to grow, reaching its present 89 acres.  In December 2003, the Zoo name was officially changed from the Jacksonville Zoo to the Jacksonville Zoo and Gardens. The Zoo is in the process of becoming officially recognized as a botanical garden.

One of the Zoo's most significant, early animal purchases was a female Asian elephant, "Miss Chic," bought in 1926 with money raised by local school children. The other most significant animal in the Zoo's history was a jaguar named "Zorro."

Zorro was a male, wild-born black (or "melanistic") jaguar that arrived at the Zoo in August 1967. At that time, black jaguars were very rare in captivity. Zorro was at the  Zoo until his death in September 1986. During his time he produced many kittens that were sent to other zoos across North America. When investigated in the spring of 2003, there was not a current North American captive born black jaguar that was not a descendant of Zorro.

By the end of the 1960s, the Zoo was reputed to have the largest collection of exotic animals in the Southeast, but it had fallen on hard times and a great deal of money was needed to save the Zoo. Community leaders, under the direction of Mayor Hans Tanzler, appointed a seven-member committee to search for an alternative to closing the Zoo.

The Jacksonville Zoological Society subsequently came into being in April 1971, having grown from the seven-member committee to 85 of the city's most influential leaders. The Society began managing the Zoo on June 21, 1971.

The City of Jacksonville contracts with the Society to manage all phases of the operation of the Zoo. All property, including animals, equipment, and all improvements, belong to the city, which in turn contributes an annual subsidy to offset some of the Zoo's operating expenses. All other Zoo expenses are paid through revenues earned from admissions, concession sales, memberships, the Animal Care Club program, group sales, the Annual Fund, sponsorships, grants and several fundraising events. The Zoo serves a two-state area within a 100-mile radius of the facility.

A major redevelopment of the Zoo began in 1992. Through a combination of River City Renaissance funds and donations from the private sector, $22.5 million has been raised to complete Phase One of the Master Plan. Projects completed include a new front entry gate and parking lot, the Main Camp entrance, Birds of the Rift Valley Aviary, Great Apes, an expanded train ride, an elephant and breeding complex, RiverBranch Foundation Animal Medical Center, the PepsiCo Foundation Education Campus, and redevelopment of the 11-acre Plains of East Africa.