Ultra‐endurance sports are growing in popularity but can be associated with adverse health effects, such as exercise‐induced muscle damage (EIMD), which can lead to exertional rhabdomyolysis. Circulating microRNAs (miRNAs) may be useful to approach the degree of EIMD. We aimed to (1) investigate the relevance of circulating miRNAs as biomarkers of muscle damage and (2) examine the acute response of skeletal/cardiac muscle and kidney biomarkers to a 24‐h run in elite athletes. Eleven elite athletes participated in the 24‐h run World Championships. Counter‐movement jump (CMJ), creatine kinase (CK), myoglobin (Mb), creatinine (Cr), high‐sensitive cardiac troponin T (hs‐cTnT), and muscle‐specific miRNA (myomiR) levels were measured before, immediately after, and 24 and 48h after the race. CMJ height was reduced immediately after the race (−84.0 ± 25.2%, p < 0.001) and remained low at 24 h (−43.6 ± 20.4%, p = 0.002). We observed high CK activity (53 239 ± 63 608 U/L, p < 0.001) immediately after the race, and it remained elevated 24h after (p < 0.01). Circulating myomiR levels (miR‐1‐3p, miR‐133a‐3p, miR‐133b, miR‐208a‐3p, miR‐208b‐3p, and miR‐499a‐5p) were elevated immediately after the 24‐h run (fold changes: 18–124,723, p<0.001) and significantly (p < 0.05) correlated or tended to significantly (p < 0.07) correlate with the reduction in CMJ height at 24 h. We found no significant correlation between CMJ height loss at 24 h and CK (p = 0.23) or Mb (p = 0.41) values. All elite ultramarathon runners included in our study were diagnosed with exertional rhabdomyolysis after the 24‐h ultramarathon race. MyomiR levels may be useful to approach the degree of muscle damage.