Background: The term Fetal Alcohol Spectrum Disorders (FASD) describes a range of neurodevelopmental conditions, the direct result of prenatal alcohol exposure. FASD encompasses a range of behavioural, cognitive and sleep patterns that are sometimes indiscernible from other neurodevelopmental conditions, one in particular being Autism Spectrum Disorders (ASD). This study aimed to provide a comparison of behavioural, cognitive, affect-related and sleep profiles in children aged between 6 and 15 years with diagnoses of FASD or ASD, in contrast to typically developing (TD) children. Methods: We compared 29 children with FASD, 21 children with ASD and 45 typically developing (TD) children on parental-reported questionnaires measuring behaviour and executive functioning: the Child Behaviour Checklist (CBCL), the Spence Children’s Anxiety Scale (SCAS) and the Behaviour Rating Inventory for Executive Function (BRIEF). Additionally, parents completed the Children’s Sleep Habits Questionnaire (CSHQ), and children wore actigraphy watches while sleeping to objectively capture their sleep habits. The three groups were compared using ANCOVA, controlling for age effects. Results: Children with FASD scored significantly higher than the other two groups on the CBCL subscales of attention problems, somatic complaints, social problems, delinquency, and aggressive behaviour, as well as the panic subscale of the SCAS. Children with FASD also scored higher on all measures of the BRIEF than the ASD and TD groups, indicating greater problems with working memory and more difficulty shifting between tasks, planning, organising, inhibiting their behaviour and exercising emotional control. Nocturnal sleep duration in children with FASD was reported as one hour less than TD children and 46 minutes less than children with ASD per night. Conclusions: The findings in this study highlight several syndrome specific features (shorter sleep duration, executive functioning difficulties, and higher levels of social and behavioural problems and panic) that potentially contribute to the unique phenotype of FASD. Whilst this research highlights the need for further work in this area, initial clinical screening for FASD should take such data on discernible characteristics, particularly the syndrome specificity of the BRIEF, into consideration.