Background Fetal alcohol spectrum disorder (FASD) is one of the most common causes of preventable intellectual disability, and the key associated deficits are in executive function (EF). Aspects of EF can be improved using cognitive training interventions. The highest prevalence of FASD globally (at a rate of 135.1 per 1000) has been found in a South African population in the Western Cape province. There is a shortage of specialized health service personnel, and there are limited remedial services. Computer-based cognitive training, if age and culturally appropriate, could be an effective way to provide the interventions with minimal need for skilled personnel and other resources. The Foundation for Alcohol Related Research has developed such a program for the South African context. Objective This protocol aimed to evaluate whether it is feasible to use computerized cognitive training in a resource-poor context to improve cognitive function in children exposed to alcohol in utero. Methods We are conducting a randomized controlled trial in the Saldanha Bay Municipal area, evaluating a custom-developed cognitive training program to improve the cognitive function of children aged between 4 and 6 years who were exposed to alcohol in the prenatal stage. Participants will be recruited from local Early Childhood Development centers. Community workers will interview biological mothers to identify alcohol-exposed pregnancies. Alcohol-exposed children will be randomized into an intervention or a control group of 40 participants each using block randomization. A group of 40 children not exposed to alcohol will be included in a normative group using individual randomization. The intervention group will play the game for 6 months (40 sessions). Normative and control groups will receive no intervention. Neurodevelopmental assessments will be done at baseline and upon completion of the study with all participants. Results The intervention has started, and all baseline assessments have been done at the time of submission. Conclusions This study will provide insight into whether computerized cognitive training is viable and effective in the South African context. It has the potential to provide a means of intervention globally and in other resource-poor context and expand the knowledge base regarding executive functioning and FASD. This paper presents the research protocol and intervention design of the study. Trial Registration ISRCTN Registry ISRCTN17244156; http://www.isrctn.com/ISRCTN17244156. International Registered Report Identifier (IRRID) DERR1-10.2196/14489