Commencing operation on 1 January 2019 as the Department of Transport (DOT), the DOT was formed in machinery of government changes made by Premier Daniel Andrews after the re-election of his Labor government at the 2018 Victorian state election.

[9][10] The new department was formally established on 1 January 2019, with Paul Younis as acting Secretary.

Government ministers claimed that the merger was a more modern approach to integrated transport planning; however, media reports and the state Opposition suggested that the changes were an attempt to reduce transparency and obscure cost overruns on major projects.

[12][13][14] The Public Transport Users Association offered its cautious support for the changes, saying that although integration of planning functions was a positive, the merger risked creating an entrenched and inaccessible bureaucracy.

It is led by Director-General Kevin Devlin who is responsible to the Minister for Transport and Infrastructure, Danny Pearson.

[17] On 2 April 2024, the MTIA merged with Victorian Health Building Authority (VHBA) to form Victorian Infrastructure Delivery Authority (VIDA) and includes health infrastructure such as hospitals in its scope.

The Suburban Rail Loop Authority (SRLA) was established in September 2019 as an administrative office of the DOT.