This study examines the conceptual relationship between scientific thinking and inquiry-based learning in science education, in light of the widespread adoption of inquiry-oriented approaches as a means of developing learners’ scientific thinking. However, despite this prevalence, the educational literature often presents the relationship between the two as a direct causal link without sufficiently analysing the epistemological and pedagogical foundations that make such integration feasible within the school context. Against this background, the study aims to re-examine this relationship from a critical, conceptual, analytical perspective. It seeks to dismantle the simplifying assumptions that reduce inquiry to a set of classroom procedures, which are detached from the cognitive structure of scientific practice. It shows that reducing inquiry to procedural activities may weaken its capacity to support scientific thinking because it disconnects inquiry from the epistemic and argumentative dimensions that characterise the construction of scientific knowledge. From this standpoint, the study argues that the relationship between scientific thinking and inquiry-based learning cannot be understood as a direct causal relationship, but rather as a conditional structural relationship involving a set of interrelated factors. Accordingly, the study proposes a conceptual framework that contextualises inquiry as a cognitive practice involving constructing scientific problems, formulating hypotheses, analysing evidence, engaging in scientific argumentation and practising epistemic reflection. This contributes to a more integrated theoretical understanding of the relationship between inquiry and scientific thinking in science education.