Previous research has underlined the importance of school students’ engagement in science (including students’ attitudes, interests and self beliefs). Engagement in science is important as a correlate of scientific literacy and attainment, and as an educational outcome in its own right. Students positively engaged with science are more likely to pursue science related careers, and to support science related policies and initiatives. This retrospective, secondary analysis of PISA 2006 national data for Aotearoa New Zealand and Australia examines and compares the factors associated with science literacy and with science engagement for indigenous and non-indigenous 15 year old students. Using a four step hierarchical regression model, our secondary analyses showed consistent patterns of influence on engagement in science for both indigenous and non-indigenous students in Aotearoa and Australia. Variations in students’ interest, enjoyment, personal and general valuing, self-efficacy, and self concept in science were most strongly associated with the extent to which students engaged in science activities outside of school. In contrast, socioeconomic status, time spent on science lessons and study, and the character of science teaching experienced by students in their schools were the factors most explanatory of variations in science literacy. Yet, the factors that explained variation in science literacy had only quite weak associations with the suite of variables comprising engagement in science. We discuss the implications of these findings for science educators and researchers interested in enhancing students’ engagement with science, and committed to contributing positively to closing the persistent gap in educational outcomes between indigenous and non-indigenous peoples.