The zoo originally began in 1894 as Riverview Park Zoo. Just four years later it had over 120 animals. In 1952, the Omaha Zoological Society was created with aims to improve the zoo.
In 1963, Margaret Hitchcock Doorly donated $750,000 (approximately $4.5 million in 2005 dollars). In doing so, she stipulated that the zoo be renamed in memory of her late husband, Henry Doorly, chairman of the World Publishing Company.
Union Pacific helped the zoo lay down 2.5 miles (4.0 km) of track in 1968 with the inaugural run of the Omaha Zoo Railroad made on July 22, 1968.
The Lied Jungle opened on April 4, 1992 at a cost of $15 million. It is the largest indoor rainforest in the world; it occupies an 80 foot tall building that spans 1.5 acres and is located just inside the main entrance.