Autism Spectrum Disorder (ASD) is comprised of a group of heterogeneous neurodevelopmental conditions, typically characterized by a triad of symptoms consisting of (1) impaired communication, (2) restricted interests, and (3) repetitive and stereotypical behavior pattern. An accurate and early diagnosis of autism can provide the basis for an appropriate educational and treatment program. In this work, we propose a computational model using a Multilayer Fuzzy Cognitive Map (hereafter referred to as MFCM) based on standardized behavioral assessments diagnosing the ASD (MFCM-ASD). The two standards used in the model are: the Autism Diagnostic Observation Schedule, Second Edition (ADOS2), and the Autism Diagnostic Interview Revised (ADIR). The MFCM’s are a soft computing technique characterized by robust properties that make it an effective technique for medical decision support systems. For the evaluation of the MFCM-ASD model, we have used real datasets of diagnosed cases, so as to compare against other method/approaches. Initial experiments demonstrated that the proposed model outperforms conventional Fuzzy Cognitive Maps (FCMs) for ASD diagnosis. Our MFCM-ASD model serves as a diagnostic tool required to support the medical decisions when determining the correct diagnosis of Autism in children with different cognitive characteristics.