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Background: There is an overabundance of claims about the advantages and disadvantages of health interventions. Many people are unable to assess the reliability of these claims. Acting on unreliable health claims or failing to act on reliable advice can lead to waste of resources and unnecessary suffering. There is a global focus on teaching critical thinking, including in the new Kenyan curriculum, however, critical thinking about health is not taught in Kenyan schools. The study planned for in this protocol is an evaluation of the effects of the Informed Health Choices secondary school intervention on the ability of lower secondary school students in Kenya to think critically about health information and choices. The intervention consists of providing teachers with digital teaching resources and training them to deliver the intervention to students. The intervention covers 10 lessons that address nine key concepts. Methods: This study is a cluster-randomized trial. We will stratify lower secondary schools by ownership and geographical location, and randomly select 80 of them. We will randomly allocate the schools to either the intervention or control group. The intervention schools will teach the 10 lessons in one academic term alongside the Kenya national secondary school curriculum. The control schools will continue teaching the national secondary school curriculum. The primary outcome measure will be a test with multiple-choice questions from the Claim Evaluations Tools item bank. The test will include two items for each of the nine concepts covered by the teaching resources. The primary outcome will be the proportion of students attaining a predetermined passing score. Trial registration: Pan African Clinical Trial Registry, trial identifier: PACTR202204883917313. Registered on 05/04/2022.