It is generally accepted by researchers, policy-makers and practitioners that progress in Indigenous education depends on working in partnership with Indigenous people, and that programs and services are best provided in partnership. The 2014-2016 Whole of Community Engagement initiative built a partnership of non-Indigenous researchers with researchers, teachers, education leaders and elders from six remote Northern Territory Aboriginal communities. In this paper we describe the features that led us to characterise the initiative and the remote community and school context as intercultural and complex. The former included methodology, staffing, meeting procedure and interpersonal communication, negotiation of meaning and decision-making. On the basis of this approach, we found that intercultural complexity was strongly evident in schooling in Galiwin'ku, Elcho Island, North East Arnhem Land, which was the community most closely studied by the authors. The paper contributes to the recognition of intercultural complexity in remote Aboriginal schooling, and the potential benefit that its recognition can have for educational outcomes in those contexts.