Background: The Informed Health Choices (IHC) network is a group of researchers aiming to develop the public’s critical thinking skills and help them make informed health choices. We started with young people and developed the primary and secondary school resources for teaching critical thinking about health choices. The “Be Smart about your Health” secondary school resources are designed for lower secondary students and will be evaluated in randomized trials in three countries: Kenya, Rwanda, and Uganda. This protocol is for a process evaluation that will be conducted alongside the trial in Rwanda. The aim is to assess the implementation process, impacts of the intervention, and factors affecting the impacts and scaling up use of the resources. Methods: We will follow the UK Medical Research Council’s guidance for designing process evaluations of complex interventions alongside randomized trials. We will use quantitative and qualitative methods. We will collect quantitative data to assess lessons taught (dose), students’ attendance (reach) and any alterations in how the intervention (adaptation) is delivered in all schools allocated to the intervention arm (n=42). We will explore the intended and unintended effects, and transfer of learning through focus group discussions (FGDs) with students (n=8-10 FGDs), their parents/guardians (n=5 FGDs) and their teachers using key informant interviews (KIIs) (n=8-10 KIIs). We will also explore factors affecting the effective delivery and scaling up of the intervention through interviews with teachers (n=8-10 KIIs), school administrators (n=8-10 KIIs), district authorities (n=5 KII) and policymakers in education (n=5 KIIs). We will collect qualitative data in about 8-10 schools varying by district, school ownership, and school performance. We will analyse quantitative data using descriptive statics and qualitative data using thematic content analysis and framework analysis.