I examine how teachers employ a questioning strategy in supporting Grade 9 learners doing science investigations in South African schools. A particular focus of this study was how teachers use questioning in contributing towards the autonomy of these learners. The research adopted a qualitative approach which involved the collection of data by means of classroom observations and interviews with five teachers at schools resourced for practical work. The analysis of transcript data revealed that teachers support learners by asking probing questions at all stages of the investigation. The teachers used a questioning strategy in enabling the learners to understand more clearly the question or hypothesis they intended investigating, to review and reconsider their planning, to rethink some of their actions when collecting data, to make sense of their data, and to revisit and amend their plan after generating incorrect findings. The significance of this study, in making explicit teacher questioning at the stages of the investigation, is that it provides a guideline for teachers on how to support learners attain greater autonomy in doing science investigations.