Background This study examined the efficacy of the Comprehensive Early Intervention for Toddlers with Autism (CEITA) program for children with autism spectrum disorders in Malaysia. Methods A randomized control trial design was adopted, in which 16 children (mean age= 34.25 months) were assigned to either the intervention group (n=8) or the control group (n=8). Children in the intervention group underwent three months of low intensity (2hrs/week) CEITA program intervention, whereas the control group received no treatment. Autism symptoms and developmental growth scores were measured at baseline, post-treatment, and 6-week follow-up to evaluate the efficacy of the CEITA program. Results Multivariate analysis of covariance results showed a significant intervention effect, whereby autism symptoms were significantly reduced (η2 = 0.36), and growth scores for all developmental domains (η2 = 0.20-0.66) were significantly increased. Conclusion Hence, this study highlights the potential of the CEITA program’s clinical implications, and relevant future research is recommended. Trial registration Reg number: NMRR ID-22-00626-8LB, dated 29th April 2022.