Background Despite growing evidence of deleterious health outcomes associated with sedentary behavior, prolonged static sitting in classrooms remains ubiquitous in primary schools. Sedentary behavior is associated with the development of cardio-metabolic conditions and poor back health. Preventative strategies to reduce sedentary behavior and its negative health effects may be required in a resource-constrained environment such as South Africa. Objective The primary objective of this study is to assess the feasibility of conducting a full trial to evaluate the effects of a multifaceted intervention comprising novel multifunctional classroom furniture and a video-based curriculum versus usual care on sedentary behavior among students aged 10-11 years in primary schools. The secondary objective is to assess the preliminary effects of the intervention on sedentary behavior and postural dynamism. Methods Eighty grade 5 or 6 students, aged 10 and 11 years, in mixed-gender schools within the Western Cape metropolitan urban area in Cape Town, South Africa are eligible to participate in this pilot cluster stepped-wedge trial design with classroom as the unit of randomization. Data will be collected at the schools. The intervention will comprise multifunctional classroom furniture that allows for sitting and standing as well as a video-based curriculum on sedentary behavior. Usual practice is the absence of the intervention. The primary outcomes assessed will be (1) adherence to the intervention and (2) project pragmatics. The secondary outcomes will be (1) sedentariness measured using activPAL3 microsensors and (2) postural dynamism measured using Noraxon Myomotion inertial measurement units. We randomized the school to the first or second start of the intervention. This is an open-label trial and therefore blinding will not be possible for any group. Descriptive analysis of the feasibility and physiological outcomes will be presented. We will report the preliminary estimates of the effects of the intervention on sedentariness and postural dynamism using the mean difference and 95% CI. Results At the time of submission, two classrooms have been recruited into the study. Baseline physical activity and postural dynamism data have been collected from 10 participants from each class. Conclusions The results of this feasibility stepped-wedge cluster randomized controlled trial will be useful in informing the design of the main trial to assess whether this multifaceted intervention of multifunctional classroom furniture that allows for sitting and standing as well as a video-based curriculum versus usual care has any effect on sedentary behavior in low-resource-setting primary schools. Trial Registration Pan African Trials Registry PACTR201811799476016; https://tinyurl.com/y4upoys8 International Registered Report Identifier (IRRID) RR1-10.2196/18522