A sedentary lifestyle and Olympic participation are contrary risk factors for global mortality and incidence of cancer and cardiovascular disease. Extracellular vesicle miRNAs have been described to respond to exercise. No molecular characterization of young male sedentary people versus athletes is available; so, our aim was to identify the extracellular vesicle miRNA profile of chronically trained young endurance and resistance male athletes compared to their sedentary counterparts. A descriptive case–control design was used with 16 sedentary young men, 16 Olympic male endurance athletes, and 16 Olympic male resistance athletes. Next‐generation sequencing and RT‐qPCR and external and internal validation were performed in order to analyze extracellular vesicle miRNA profiles. Endurance and resistance athletes had significant lower levels of miR‐16‐5p, miR‐19a‐3p, and miR‐451a compared to sedentary people. Taking all together, exercise‐trained miRNA profile in extracellular vesicles provides a differential signature of athletes irrespective of the type of exercise compared to sedentary people. Besides, miR‐25‐3p levels were specifically lower in endurance athletes which defines its role as a specific responder in this type of athletes. In silico analysis of this profile suggests a role in adaptive energy metabolism in this context that needs to be experimentally validated. Therefore, this study provides for the first time basal levels of circulating miRNA in extracellular vesicles emerge as relevant players in intertissue communication in response to chronic exercise exposure in young elite male athletes. Highlights An extracellular vesicle miRNA profile defined by next‐generation sequencing differentiates athletes compared to sedentary young males. Extracellular vesicle miR‐16‐5p, miR‐19a‐3p, and miR‐451a were lower in athletes irrespective of their sport disciplines compared to sedentary young males. Extracellular vesicle miR‐25‐3p was specifically lower in endurance athletes compared to sedentary young males. Energy metabolism and structural pathways are the main regulated ones based on extracellular vesicle miRNA profile.