The Maleny Neighbourhood Centre began before 1990 when a group of concerned Maleny residents recognised the need to develop responses to the growing needs of families, young people, and people with special needs. The organisation was incorporated in 1994 and became the first community association in Maleny that had a specific purpose to address poverty and social disadvantage in the area. The Maleny Flexi School came into existence in 2002 and has been co-located with Maleny Neighbourhood Centre ever since.

The first space occupied by Maleny Neighbourhood Centre and Maleny Flexi School was in the RSL Hall. Over the years, the centre moved to several locations, growing programmes and community support. In 2010, Maleny Neighbourhood Centre became the leaseholders of a purpose built centre at 17 Bicentenary Lane, provided by the Queensland Government Department of Communities. The building is on land owned by Sunshine Coast Council.