The scientific evidence supports that physical inactivity in childhood is a reality throughout the world which generates important consequences in the global development of children. Young people with Autism Spectrum Disorder (ASD), due to the characteristics of the disorder they suffer, constitute a group at risk. Therefore, assessing the levels of physical activity (PA) in this group is fundamental for subsequent decision making and implementation of PA promotion programmes. Consequently, the aim of this systematic review was to identify, summarise and analyse the main instruments used to assess the levels of PA (in terms of time and/or intensity) in primary school children diagnosed with ASD. Scientific articles in English and Spanish published in five databases were reviewed: PsycINFO, WOS, SPORTDiscus, Scopus and PubMed, following the guidelines of the PRISMA statement. Out of the 605 articles identified, 12 met the previously established inclusion criteria. The instruments used by the studies analysed were divided into two main groups: accelerometers and questionnaires. Both showed different strengths and limitations but agreed on the low levels registered of PA in children with ASD. For this reason, it is considered necessary that further research be carried out in this field, as well as the development and implementation of sports programmes adjusted and adapted to the needs and characteristics of the ASD group.