© 2020, The Author(s). Children and young people with rare and inherited diseases will be significant beneficiaries of genome sequencing. However, most educational resources are developed for adults. To address this gap in informational resources, we have co-designed, developed and evaluated an educational resource about genome sequencing for young people. The first animation explains what a genome is, genomic variation and genome sequencing (“My Genome Sequence”: http://bit.ly/mygenomesequence), the second focuses on the limitations and uncertainties of genome sequencing (“My Genome Sequence part 2”: http://bit.ly/mygenomesequence2). In total, 554 school pupils (11–15 years) took part in the quantitative evaluation. Mean objective knowledge increased from before to after watching one or both animations (4.24 vs 7.60 respectively; t = 32.16, p < 0.001). Self-rated awareness and understanding of the words ‘genome’ and ‘genome sequencing’ increased significantly after watching the animation. Most pupils felt they understood the benefits of sequencing after watching one (75.4%) or both animations (76.6%). Only 17.3% felt they understood the limitations and uncertainties after watching the first, however this was higher among those watching both (58.5%, p < 0.001). Twelve young people, 14 parents and 3 health professionals consenting in the 100,000 Genomes Project reported that the animation was clear and engaging, eased concerns about the process and empowered young people to take an active role in decision-making. To increase accessibility, subtitles in other languages could be added, and the script could be made available in a leaflet format for those that do not have internet access. Future research could focus on formally evaluating the animations in a clinical setting.