Background: Males are diagnosed with Autism Spectrum Disorder (ASD) approximately four times as often as females. This has led to interest in recent years of potential under-diagnosis of females, as well as negative consequences for females with ASD due to under-identification. A number of potential explanations for gender bias in diagnosis are discussed including that females and males may present differently despite showing the same core symptoms. Previous research has shown inconsistent findings in comparisons between genders in young children with ASD for whom early intervention is vital. Thus, the aim of the present study was to investigate the social, communication, and cognitive functioning, as well as level of ASD symptoms, in a cohort of children who presented for early intervention to inform understanding of gender differences in this population, as well as to inform understanding of the mechanisms by which gender bias may occur. Method: Participants included 254 children (42 females) aged 29–74 months who completed measures of cognition, communication skills, adaptive behaviour, and ASD symptoms on entry to early intervention. Results: Consistent with hypotheses, no significant gender differences were found both overall, and when split by functioning level. However, a similar ratio of males and females was found in both high- and low-functioning groups contrary to predictions. Conclusions: These results are consistent with some of the previous research that suggests gender differences may not be apparent in clinical samples at this young age. We highlight a need for further research that may use universal screening or longitudinal methods to understand the trajectory of development for females with ASD specifically. Such research could better inform timely and tailored intervention from the preschool years onwards.