Wa Ora Montessori School began as an idea in the minds of a few Wellington parents in 1987. Their children were nearing the end of Montessori preschool and no Montessori primary school existed for children to continue their unique education. The parents began a series of regular meetings to gauge public support and plan for the school which was to be the first stand-alone Montessori primary school in New Zealand.

Two Wellington sites were investigated, one at the Rigi in Kelburn and the other at Kingston where a Montessori preschool is now located. However, neither site was suitable. The then-Wellington Education Board offered the empty IHC workshop on the Wa Ora Special School site. It was ideal in many ways, although out of its original base in Wellington; it was available for a peppercorn rental and had the space to expand, especially as the other block on the site (used by special needs students) was likely to be available at a later date.

By the time the first class began operation in May 1988, the establishment committee had set out the original goals and objectives of the school, set up the school as an incorporated society, established a broad curriculum and formulated the constitution. The committee consisted of Pip and Antony Fowler, Nicky Chisnall and Dave Stott, Debbi and Ian Carson, Vicky and Sidney Zdrahal, Dayal Drane and Susannah Engel and Ruth van Berkel.

Although the main aim of the committee was to provide a primary school, the location allowed two 3-6 classes as well. Logically, the 3-6 classes could feed the primary class. Also Wa Ora was to be the first Montessori preschool in the Hutt Valley, fulfilling a need in the area.

In May, 1988 the first class opened as the Kowhai Room with 11 students. Nicky Chisnall was the teacher with Claudia Duncan as assistant, and Debbi Carson as administration officer. In the third term of 1988, and after an enormous amount of work by parents and committee to upgrade a badly run-down facility and supply the school with equipment, the primary class and a second 3-6 class were opened.

Debbie Senoff Langford was appointed principal and teacher of the primary (6-9) class. Although coming from Chicago, Debbie had taught in New Zealand previously. The second 3-6 class opened with Californians, Susan Costello as teacher and Jaylene Hogan, who joined the class at the beginning of 1989, as assistant. Claudia Duncan became the teacher of a third 3-6 class in 1990.

By 1991 demand for another class coincided with the demise of Wa Ora Special School. Wa Ora Montessori School took over what is now the primary block. The school now consisted of three 3-6 year programmes and two primary classes, 6-9 years and 9-12 years.

In 1992 the 3-6 playground was extensively upgraded. 1992 also saw the school finally accomplish purchase of the site from the Ministry of Education. This allowed the pursuit of integration for the primary school.

In early 1993 both the 3-6 and the primary block were renovated and expanded. Mezzanine floors and outside verandahs, designed by architect and parent Wendy Harding, were added to the 3-6 block.

In September 1993, Wa Ora's primary school finally integrated into the state school system. Integration has meant payment of teacher salaries and running costs being paid by the State, and has allowed a large drop in school fees for parents. Integration had been investigated by the establishment committee in 1988, but was unattainable until the school was able to purchase the school site. Integration has not compromised Wa Ora's special character, the Montessori philosophy. In 1995 a mission statement was written by the BOT, Council, Staff and interested parents. It has reaffirmed the special character of the school and defined the focus for the school community.

In 1998/1999, the three primary classrooms were rennovated and several resource room/offices were created to utilise the available space more effectively. The entrance/reception office became a welcoming feature of the school. Two new preschool classrooms were built. The buildings were officially opened on Tuesday 25th May, 1999. 

 With steady growth in the school roll, it become obvious in 2006 that the current 9-12 class was too small. Planning started on the development of a new classroom.  2008 saw the opening of completely new 9-12 classroom called Totara.

As a result of parent surveys and strategic planning sessions, a decision was made to start an adolescent program (12-15).  In 2008 an application was made to the ministry for a "change of class" to allow the school to have a secondary school component and this was successful.  Hence in 2009 Wa Ora started its adolescent programme with 8 students.

In 2009 and 2010, the junior school playground was upgraded with the addition of an outside storage facility and raised gardens.

In 2010 an upgrade to the 6-9 classrooms was completed increasing the size of each classroom significantly.