Researchers have noted a persistent decline in Australian students’ participation in senior science in secondary school (Year 12). Aboriginal and Torres Strait Islander (Indigenous) students are significantly less likely to continue with science, in part because western science and the present science curriculum have ignored and delegitimized Indigenous knowledges and cultures as “unempirical.” Moreover, Indigenous students who sit at multiple marginalized science identities (i.e., girls, low socio-economic background) may be less likely to continue with science. Drawing on expectancy value theory and considering intersectional identity, this study examined the extent to which Indigenous students’ science self-efficacy, intrinsic value, and utility value predicted their Y12 science enrolment and science subject selection, and if these associations were moderated by gender or socio-economic status. Multi-class logistic regression and multi-group path analysis were conducted with n = 334 Indigenous students and n = 2,801 non-Indigenous students. Utility value predicted Y12 participation and self-efficacy predicted science subject selection for Indigenous students. Socio-economic status was a significant moderator. Findings suggest that particular attention should be paid to these factors to better support Indigenous students in science.