Since 2016, Indonesia has been implementing a weekly iron-folic acid supplementation (WIFAS) program in two provinces for school going adolescent girls to reduce anaemia. This study aimed to explore the awareness and understanding of school-going adolescent girls and parents regarding anaemia and WIFAS. The study was conducted in 10 districts, each from East Java province and East Nusa Tenggara province. Twenty focused group discussions (FGDs) were conducted with school-going adolescent girls (n5174) and ten FGDs with parents (n566). Also, in-depth interviews (IDIs) were conducted with school-going adolescent girls (n520) and their parents (n510) from 20 schools. All FGDs and IDIs were audio-recorded, transcribed verbatim, and analyzed for themes using NVivo Pro 12 software. School going adolescent girls and parents had high levels of misinformation about anaemia and healthy nutritional practices, which were influenced by socio-cultural milieu and local dietary habits. Both parents and girls perceived low risk of anaemia for school-going adolescent girls. Girls stated that their parents’ opinion about anaemia influenced their desire to consume iron supplements. In conclusion, girls and parents would benefit from increased access to information about anaemia risks and prevention, and the benefits of WIFAS for adolescent girls. Prevention of anemia should include relevant dietary guidance that considers their socio-cultural milieu and local dietary habits.