Introduction: Anxiety disorders are highly prevalent in individuals with autism spectrum disorder (ASD), but knowledge is limited regarding identification and treatment of these disorders in individuals with ASD and more severe levels of intellectual disability (ID). The current case study aims to explore and describe the inpatient, psychiatric assessment in an adolescent male with ASD, severe ID and self-injurious behaviour (SIB) who was diagnosed with a co-occurring anxiety disorder. The study further aims to explore the implications of this diagnosis for subsequent intervention and care, including management of SIB. Materials and methods: Case study including multimodal, psychiatric assessment and subsequent intervention. Results: Following changes in care strategies attempting to incorporate the understanding of anxiety/trauma as contributing to SIB, a reduction of SIB was observed, and this reduced frequency was maintained when the patient was discharged from the inpatient setting. Conclusions: Though no causal inferences are possible, these experiences indicate that further research is needed regarding possible associations between SIB and anxiety in individuals with ASD, including implications for treatment. Experiences from the current case further indicate that it is possible to recognize and diagnose anxiety disorder in complex cases involving ASD, severe ID, limited verbal language skills, and severe SIB.