Māori are the Indigenous peoples of Aotearoa, New Zealand, and, similar to other Indigenous populations, face significant health inequities. Of concern, Māori mothers and birthing parents experience persistent and grave mental health inequities within the perinatal period relative to other ethnic groups. Indigenous research participants who have mental illness and who are also pregnant or in the early stages of parenting present intersecting ethical dilemmas for researchers working with research participants in situations of vulnerability. Given the known historical harms that culturally unsafe research has previously caused Indigenous peoples, it is crucial that research approaches with Indigenous mothers and birthing parents who have experienced mental illness are culturally safe and ethically sound. Kaupapa Māori research provides a framework to decolonise research processes and create the conditions for the cultural safety of the researcher and research participants. Kaupapa Māori research is grounded in a philosophy of relationship and a mutual recognition of the mana (dignity, prestige) of both researcher and participant. Engaging in culturally safe and responsive research with Māori can address power imbalances and ensure that the priorities of Māori communities are centred within the research. This paper details the application of a Kaupapa Māori research methodology used within qualitative research with Māori mothers and birthing parents experiencing perinatal mental illness and is structured in three parts. The first section situates Kaupapa Māori methodology in relation to the context of Māori mothers and birthing parents experiencing perinatal mental illness, providing a rationale for the research. The second section describes the application of Kaupapa Māori methodology within the research project. The third section discusses Kaupapa Māori methodology’s influence on research participants’ cultural safety through a case study format.