Noise hypersensitivity is a poorly understood symptom of Autism Spectrum Disorder (ASD). For some, problem behaviors co-occur with the aversive noise. Limited literature exists on treating noise hypersensitivity; however, noise hypersensitivity may be related to a specific phobia. This case study utilizes modified Cognitive Behavioral Therapy (CBT) to address anxiety, avoidance, and problem behaviors evoked by noise in a teen with ASD and mild Intellectual Disability (ID). Using multi-method assessment and individualized treatment, problem behaviors reduced, and independent coping strategies use occurred. Successful desensitization supports the efficacy of modified CBT as a treatment for noise-related anxiety and problem behaviors in individuals with ASD and ID. Outcomes are discussed considering intervention difficulties for noise hypersensitivity in a complex and diverse population.