Purpose: This study aims to analyse the relationship between Inquiry-Based Learning (IBL), Learning Engagement (LE) and Scientific Literacy (SL) amongst primary school pupils, with a focus on the mediating role of learning engagement in the relationship between inquiry-based learning and scientific literacy. Method: The study employed a quantitative approach using an explanatory survey design involving 250 primary school pupils in Years 4–6. Data on inquiry-based learning and learning engagement were collected via a structured questionnaire, whilst science literacy was measured using a test based on scientific contexts. Analysis was carried out using Covariance-Based Structural Equation Modelling (CB-SEM) with LISREL software to test the measurement model, structural relationships and mediating effects. Findings: Inquiry-based learning is positively correlated with learning engagement (β = 0.82), whilst learning engagement is positively correlated with science literacy (β = 1.34). The direct relationship between inquiry-based learning and science literacy is negative (β = −0.39), whilst the indirect relationship via learning engagement is positive and significant (β = 1.10; t = 6.95). This difference in direction indicates a pattern of competitive mediation, with a positive total effect (β = 0.71) Significance: This study broadens our understanding of the role of learner engagement in the relationship between inquiry-based learning and science literacy. The study identifies a competitive mediation pattern in which Inquiry-Based Learning is negatively associated with Scientific Literacy through the direct pathway but positively associated with it through Learning Engagement. This finding contributes to understanding the complexity of relationships among inquiry-learning experiences, student engagement, and scientific competence in primary education. However, the results should be interpreted as statistical associations rather than evidence of a causal mediation mechanism.
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