Background We designed the “Be smart about your health” digital resources to teach lower secondary school students how to assess the trustworthiness of claims about the effects of treatments. We shall evaluate effects of using these resources in a randomised trial in Uganda. This paper describes the process evaluation that will be conducted alongside this trial. The aim is to identify factors affecting the implementation, fidelity, effects, and scaling up use of the Be smart about your health teaching resources in Uganda and potential adverse and beneficial effects of the intervention. Methods Forty teachers from 40 schools in the intervention arm of the trial will complete a lesson evaluation questionnaire after each of the 10 lessons and at the end of the term. We will conduct structured classroom observations at all 40 schools. We will purposively select eight schools where we will conduct focus group discussions with teachers and students. We also will conduct key informant interviews among education officers (that visit the schools to monitor the implementation), teachers, head teachers, learners, and their parents. We will use a framework analysis approach to analyse the data. Expected results We anticipate that the findings from this evaluation will provide insights into factors that may impact the effectiveness of using the Be smart about your health resources, factors that can inhibit or facilitate scaling up use of the resources, and potential effects that were not measured quantitatively after the intervention, including transfer of what was learned to other contexts and adverse effects.