Background. Secondary chemistry requires students to transfer concepts to unfamiliar situations, interpret evidence and construct explanations. A structured design-thinking process may provide repeated opportunities to practise these behaviours. Aim. To evaluate, in a prospective school-based study, whether a six-week design thinking-based chemistry programme improves concept application and problem-solving skills compared with conventional chemistry instruction. Methods. This protocol describes a quasi-experimental pre-test/post-test comparison-group study among secondary school students. The intervention consists of six weekly cycles involving understanding a context, defining a chemistry problem, generating alternatives, developing a solution, testing evidence and revising the solution. The primary outcomes will be scores on a Concept Application Test (CAT) and a Problem-Solving Skills Test (PSST). The instruments will undergo expert review, pilot testing, reliability assessment and rubric-based scorer training before the main study. The sample size will be determined a priori using a formal power calculation. Baseline-adjusted post-test comparisons will account for clustering by class or teacher where applicable. Expected contribution. The study is designed to provide empirical evidence on a clearly specified, chemistry-specific design-thinking intervention. No synthetic or simulated observations are presented as study findings in this protocol