Individuals with autism spectrum disorder (ASD) diagnoses present not only cognitive, emotional, communicative, and social challenges but also movement issues that affect their everyday activities, learning, and leisure. The use of the square-stepping exercise (SSE), a motor program initially created to strengthen the lower limbs of older adults, is spreading because of its advantages (e.g., balance and lower limb strength improvements). A study protocol to assess the SSE effects on motor, sensory, and cognitive skills in Spanish children and adolescents between 6 and 12 years old with ASD diagnoses is presented. A randomised clinical will be performed, recruiting 52 children and adolescents with ASD who will be distributed into two groups: an experimental (n = 26) and a control (n = 26) group. The SSE sessions will be held for 9 weeks (two times per week). The main variable will be balance, which will be measured with the Movement Assessment Battery for Children 2 (MABC2), and secondary outcomes will include sensory processing, attention, and executive functions. Assessments will be carried out before and at the end of the program implementation, including an additional follow up one month later. If this program obtains positive results, it should be implemented in different settings (schools, clinics, associations, etc.) to improve the quality of movement and development in children and adolescents with ASD, as it is an easy-to-use and structured tool.