Autism Spectrum Disorder (ASD) is a complex developmental disorder that includes the way a person communicates, relates, and behaves. During the COVID-19 pandemic, ASD is one of the groups that is vulnerable to being infected with COVID-19, so it requires special attention. ASD children have different nutritional needs than normal children because ASD children have organ dysfunction and digestive enzymes. The Gluten Free Casein Free Diet (GFCF) has been shown to be of help in improving learning, cognitive function and communication skills in children with autism. Mother's knowledge has an important role in determining the quality of children's nutritional intake including gluten and casein-free diet. This study aims to describe the knowledge of mothers about a gluten and casein-free diet in ASD children and its application during the COVID-19 pandemic in Yogyakarta, Indonesia. This study used a cross sectional study design with a purposive sampling of 37 subjects in special schools and autism therapy around Yogyakarta, ID. The results showed that most of the mothers had good knowledge about a gluten and casein free diet (86.49%). Some mothers have also received information about gluten and casein-free diets (83.78%) and most of the sources of information came from the internet. The majority of ASD children in this study were still consuming foods containing gluten (86.49%) and casein (67.57%) during the COVID-19 pandemic.