The aim of this study was to compare bibliometric indicators of scientific productivity in physical activity (PA) in children and adolescents with autism (ASD) and Down syndrome (DS) in the PubMed database. A bibliometric study was conducted for the last 5 years (2017 to 2021). The data collected for each article were: year of publication, language of publication, country, journal name, and type of paper. The results showed that there was higher scientific productivity in the population with DS (20 studies) relative to their counterparts with ASD (31 studies). The language of publication in both cases was English. There were 10 countries that published on PA in ASD and 14 countries that published on DS. Overall, the greatest interest in publishing on PA in children and adolescents with ASD was in North America (6 studies), followed by Asia (5 studies) and Europe (4 studies). In the DS population it was in Europe (13 studies), North America (9 studies) and South America (4 studies). Nineteen journals were identified that published in the ASD population and 29 journals in DS. Six experimental studies were identified in ASD and 7 in DS. There was a higher scientific productivity with original studies. There was a positive trend of increasing scientific productivity over the years in both populations. We suggest the need to promote research on PA in both populations, regardless of the type of study, as it is an indicator of overall health status.