During the 1980s, specialist clinics at Mater Children’s Hospital became increasingly important; and clinic numbers increased from 25 to 42 between 1977 and 1980. These clinics covered areas including diabetes, cleft palate and cranio-facial conditions, and cystic fibrosis. In 1984, Sister Marie Fitzgerald’s Spina Bifida Clinic (the School Function Clinic), and a respiratory laboratory to help address Brisbane’s high rates of asthma in children, also opened. Three years later in 1987, Queensland's first Paediatric Sleep Unit was established at the hospital.
To support this increase in services, facilities gradually began expanding. A new McAuley wing with an infants’ ward, and The University of Queensland Department of Child Health Officers were opened. The Mater School was also constructed by the Queensland Government on land donated by the Sisters of Mercy.
The expansion of services marked Mater Children’s Hospital’s development as a large tertiary-level paediatric facility. By 1990, the emergency department was often the busiest in Queensland.
As an extension of support for families with children being cared for at the hospital, Ronald McDonald House opened on Allen Street in 1990.
Two years later, in 1992, Mater came under pressure to move Mater Children’s Hospital to Queen Elizabeth II Hospital at Mt Gravatt. In a response to the State Government, the Sisters of Mercy stated the hospital must not only remain with the Mater family at South Brisbane, but that the state should support its redevelopment.
In 1998, Queensland's first comprehensive Paediatric Epilepsy Centre was opened at Mater Children's Hospital.
The same year, on 9 March 1998 Mater opened Australia’s first private paediatric facility—Mater Children's Private Hospital. The new 25 bed hospital, based on a seaside theme, was bright and cheerful, and each patient's room had its own computer with internet access.
In 1999, Australia's first formal study into pet therapy for children in hospital commenced at Mater Children’s Hospital.