Electromyostimulation (EMS) is used to maintain or build skeletal muscle and to increase cardiopulmonary fitness. Only limited data on the molecular mechanisms induced by EMS is available and effects on circulating microRNAs (c-miRNAs) have not been reported. This study aimed to evaluate whether EMS induces long-term changes on muscle- and cardiovascular-specific c-miRNA levels. Twelve healthy participants (33.0±12.0 yrs, 7 women) performed a 20-min whole-body EMS training and a time- and intensity-matched whole-body circuit training (CT) in random order. Blood samples were drawn pre-/post-training and at 1.5h, 3h, 24h, 48h, and 72h to determine creatine kinase (CK) and miRNA-21-5p, -126-3p, -133a-3p, -146a-5p, -206-3p, -222-3p and -499a-5p levels. Muscular exertion was determine using isometric strength test, muscle soreness/pain was assessed by questionnaire. EMS participants reported higher muscle soreness 48h and 72h post-exercise and mean CK levels after EMS increased compared to CT at 48h and 72h (time×group p≤0.01). The EMS session induced a significant elevation of myomiR-206 and -133a levels starting at 1.5h and 3h after exercise. Both miRNAs remained elevated for 72h with significant differences between 24h-72h (time×group p≤0.0254). EMS did not induce changes in cardiovascular miRNAs and no elevation in any miRNA was detected following CT. Time-course analysis of muscle-damage marker CK and c-miR-133a and -206 levels did not suggest a common scheme (p≥0.277). We conclude that a single EMS session induces specific long-lasting changes of miR-206 and miR-133 involved in muscle proliferation and differentiation. A single EMS session does not affect primary cardiovascular miRNA-21-5p, -126-3p, -146a-5p, and -222-3p levels.