Due to apartheid policies, Black African learners in South Africa have been severely disadvantaged in school science. Despite policy changes to redress these historical imbalances, Black African learners continue to underperform in science. Previous research has identified motivation as a key factor that impacts performance. Achievement goal orientation is a construct of motivation that explains learning behaviour. In an attempt to address the problem of learner motivation, this study investigated the effect of inquiry-based learning on the achievement goal-orientation of grade 10 physical sciences learners at historically disadvantaged township schools in South Africa. In South Africa, the term "township" usually refers to under-developed urban areas that were historically created for "non-whites" during the apartheid era. The findings showed that the experiment group of learners who experienced inquiry-based learning significantly gained in mastery goal orientation, while the control that were taught through a traditional direct didactic approach had an insignificant change in their mastery goal orientation. From these results, it can be concluded that inquiry-based learning does support a mastery goal orientation in learners. This orientation is regarded as desirable because mastery approach goals could support positive outcomes in conceptual learning, leading to an improvement in science achievement of learners.