Autism is a developmental disorder that has become a concern in Kenya. A characteristic feature commonly seen among people with autism is the abnormal stereotype behaviours. The study analysed the efficacy of using structured physical exercises as an intervention for managing stereotype behaviours in autism. The Nairobi Autism Unit for individuals with autism was purposively selected. The adaptive exercise routine used structured teaching principles explained by Hong (2001). The Autism Treatment Evaluation Checklist was used as the main tool for collecting data. The results indicated that the physical exercises had a positive significant impact on all the four behaviour domains (Speech/ Language/ Communication, Sensory/ Cognitive awareness, Sociability and Health/ Physical behaviours) of children at the Nairobi Autism Unit. Structured physical exercise is thus recommended as a means to manage the challenging behaviour and enhance better health and wellness amongst individuals with autism. Creative methods for including physical exercises in the daily schedule for autistic individuals could be very beneficial.