Serious game-based interventions are increasingly valuable for enhancing public health by boosting vaccination knowledge and shaping young individuals' attitudes and behaviors. These tools significantly impact how young people perceive and respond to vaccinations, but it is crucial to consider their ethical implications, particularly on the neurocognitive, affective, and social aspects of youth engaging with educational technologies. This study continued a prior randomized controlled trial assessing a game-based intervention for COVID-19 vaccine education among unvaccinated 11–14-year-olds. The study retained all 32 parent-youth pairs, equally randomized into intervention and control groups. Surveys were administered before, immediately after, and two months post-intervention, with post-intervention semi-structured interviews conducted with 7 intervention dyads. The previous study showed significant improvements in vaccine knowledge and beliefs among participants. Two months later, 75% of the intervention group reported vaccinating their children compared to 37.5% in the control group. Despite the positive impact, ethical concerns were identified. Neurocognitive concerns include the game's simplicity, potentially hindering the acquisition of critical skills such as critical thinking and problem-solving. Affective concerns highlight the lack of emotional depth, potentially resulting in disengagement and inadequate emotional development. Social concerns arise from the single-player format, which may inadequately promote collaboration, empathy, and appreciation of diverse perspectives. Serious game-based interventions show promise in improving youth vaccine knowledge and uptake, highlighting the benefits of educational technologies in public health. However, their insufficient design may hinder neurocognitive, emotional, and social development, necessitating a more nuanced, ethically responsible approach to enhance their effectiveness.