Autism spectrum disorder (ASD) is a group of developmental disabilities presenting difficulties in social interaction and language and an increased occurrence of cognitive, sensory, and motor gaps. Early intervention has been reported to improve the function of children with ASD. However, motor screening for children with ASD is difficult, as there are no specific tools for identifying this specific population. This study reports the results of using the Alberta Infant Motor Scale (AIMS), which assesses gross infant motor skills from ages 0 to 18 months, as a screening tool for detecting motor developmental delay (MDD) in small children with ASD. Methods: This retrospective cohort study included all children registered at one health care organization in Israel born between 2011 and 2017 (N = 240,299). Early childhood MDD was defined as having at least one recorded developmental physiotherapy (DPT) visit before the age of 2 years. Reasons for referral to DPT and the results of using AIMS as an appropriate tool for revealing developmental delays in infants with ASD are presented. Results: ASD diagnosis was reported in 1821 children (prevalence rate 0.75%). Of those, 388 (odds ratio 4.1, 95% CI 3.6–4.6) children were referred to DPT. Children with ASD mostly received DPT for motor delays (46.19%), torticollis (19.52%), developmental delay (15.48%), and preterm birth (7.38%). The use of AIMS as an early detection tool suggests that more than 87% of children with ASD and MDD present with a developmental delay or risk for one when using this scale. Conclusions: The prevalence of ASD among children referred to DPT for MDD is higher than its prevalence within the general population. The most common reasons for a child with ASD to be referred for DPT services are MMDs. AIMS was found to be a sensitive tool to pinpoint relevant candidates for ASD screening among children treated in DPT. Possible effects of the study: The use of AIMS as a relevant assessment scale for this group of clients is recommended. Training DPTs in identifying initial ASD signs and developing their clinical reasoning abilities will increase the chance of implementing early intervention with this group of clients.