Gilles de la Tourette syndrome (GTS) and autism spectrum disorder (ASD) are two neurodevelopmental disorders with male predominance, frequently comorbid, that share clinical and behavioral features. The incidence of ASD in patients affected by GTS was reported to be between 2.9% and 22.8%. We hypothesized that higher ASD rates among children affected by GTS previously reported may be due to difficulty in discriminating GTS sub-phenotypes from ASD, and the higher scores in the restrictive and repetitive behaviors in particular may represent at least a “false comorbidity”. We studied a large population of 720 children and adolescents affected by GTS (n = 400) and ASD (n = 320), recruited from a single center. Patients were all assessed with The Yale Global Tic Severity Rating Scale (YGTSS), The Autism Diagnostic Observation Schedule (ADOS), The Autism Diagnostic Interview Revised (ADI-R), The Children’s Yale–Brown Obsessive–Compulsive Scale (CY-BOCS), and The Children’s Yale–Brown Obsessive–Compulsive Scale for autism spectrum disorder (CY-BOCS ASD). Our results showed statistically significant differences in ADOS scores for social aspects between GTS with comorbid attention deficit hyperactivity disorder (ADHD) and obsessive–compulsive disorder (OCD) sub-phenotypes and ASD. No differences were present when we compared GTS with comorbid ASD sub-phenotype to ASD, while repetitive and restrictive behavior scores in ASD did not present statistical differences in the comparison with GTS and comorbid OCD and ASD sub-phenotypes. We also showed that CY-BOCS ASD could be a useful instrument to correctly identify OCD from ASD symptoms.