The Munroe-Meyer Institute has a long history beginning as two separate programs, which ultimately combined in the late 1990s. The Hattie B. Munroe Pavilion was born out of the Society for the Relief of the Disabled, which in 1927, became known as the Orthopedic Association of Omaha. Started in 1921, by a group of doctors and supported by a women's group interested in charitable work. The success of a 1922 summer camp inspired the Society to begin seeking funds for a permanent site to house pediatric patients recovering from orthopedic surgery. In memory of his late wife, Hattie Baker Munroe, who herself had a disability, John Munroe, a former Union Pacific executive, along with Mrs. Munroe's sister, Clara Elder, offered a house and property. The Hattie Baker Munroe Home for Convalescing Crippled Children was opened in September of 1922.

In 1956, the Munroe Home accepted a 99-year lease on property at its current location, and set out to develop a children's center, a concept later achieved by working in conjunction with the adjacent Meyer Therapy Center. An addition completed in 1992, created expanded space for recreational therapy, augmentative communication, a motion analysis laboratory and other pediatric research laboratories. The addition physically linked both buildings, and though the two programs worked cooperatively since the 1950s, they remained separate and unique entities, each with its own governing board(s) and mission.

A private board constructed the Meyer Therapy Center in 1958 as a memorial to C. Louis Meyer, a long-time Omaha resident and nationally known industrialist. It functioned as a rehabilitation center for children with disabilities such as polio and cerebral palsy. In May of 1968, Meyer Therapy Center was deeded to the University of Nebraska at which time its name was changed to C. Louis Meyer Children’s Rehabilitation Institute (MCRI). MCRI’s scope was broadened to include all developmental and other long-term disabilities, and the Institute became a training center for the broad range of specialties housed therein. In 1972, MCRI became a University affiliated program (UAP) when it first received funding from the Administration on Developmental Disabilities. In 1990, the name was changed to Meyer Rehabilitation Institute.

In 1996, the Hattie B. Munroe Foundation and UNMC signed an affiliation agreement and the previously separate Meyer and Munroe Boards, in an effort to recognize the major contributions of the Hattie B. Munroe Foundation to the previously renamed Meyer Rehabilitation Institute, voted to combine their efforts as a single board and voted to become the Munroe-Meyer Institute (MMI) for Genetics and Rehabilitation in recognition of the expanded and joint commitment to children and youth with disabilities.

The Munroe-Meyer Institute has exceptional facilities. The physical plant is extensive and is barrier free and fully compliant with all ADA and 504 requirements. The Institute consists of five buildings totaling 120,684 square feet. Additions to the H.B.M. Pavilion completed in 1990 (22,000 sq. feet) and 1998 (30,000 sq. feet), funded by the Hattie B. Munroe Foundation, house an augmentative communications program, a motion analysis laboratory, expanded recreational therapy programs and state-of-the-art basic research laboratories in molecular genetics.

In order to enhance the services and supports provided at MMI, the Institute purchased and renovated an additional building in 2001. The "MMI Diagnostic Center" has interdisciplinary and specialty clinics in a barrier-free and easily accessible environment. In 2006, the Institute totally renovated more than 7,000 square feet on the first floor of the H.B.M. Pavilion to create a new Center for Autism Spectrum Disorders and a Center for Pediatric feeding Disorders. This space includes state-of-the-art equipment to provide diagnostic and intervention services, as well as to conduct applied research and to train interdisciplinary students.