It was established on 1 February 2013, after the House of Representatives passed the Callaghan Innovation Bill the previous year.

[3] The institute takes its name from Sir Paul Callaghan, a prominent New Zealand physicist who died in 2012.

On 6 January 2014 the departments of carbohydrate chemistry[5] and high temperature superconductors[6] were ceded to Victoria University of Wellington, being renamed the Ferrier and Robinson Research Institutes respectively.

Prime Minister Christopher Luxon and Minister of Science, Innovation and Technology Judith Collins announced the government's intention to close Callaghan Innovation in a "state of the nation" speech on 23 January 2025.

[8] In mid February 2025, the Public Service Association reported that Callaghan Innovation was proposing slashing 63 jobs in response to Government plans to disestablish the organisation.