Myocarditis prognosis varies substantially, hence identification of novel prognostic factors is crucial. The prognostic role of ultra-short heart-rate variability (HRV) in myocarditis remains unknown. In a retrospective study, adult patients admitted to a tertiary hospital due to clinically suspected myocarditis were included. Clinical, laboratory and HRV parameters were assessed as predictors of severe short term complications (heart failure (HF), dilated cardiomyopathy—DCM, ventricular arrhythmia—VA and death), utilizing logistic regression (LR). Accuracy was evaluated with receiver operating characteristic (ROC) curve area under the curve (AUC). HRV indices included standard deviation of normal beat intervals (SDNN) and root mean square of successive differences (RMSSD). 115 patients, aged 34 (±13) years old, were examined. Six patients (5%) developed severe HFrEF. RMSSD was included in a multivariate LR model (RMSSD < 10.72 ms adjusted odds ratio (AOR) 14.056, p-value 0.024). Model classification accuracy was very good, with an AUC of 86%. Eight patients (7%) developed DCM. RMSSD < 10.72 ms was included in a multivariate classification model (AOR 8.826, p-value 0.013); model classification AUC of 82%. HRV did not predict development of VA or death. SDNN and especially RMSSD may be prognostic indicators in myocarditis.