INTRODUCTION: Covid-19 is a viral airway and systemic infection which can negatively affect the function of the autonomic nervous system. Cardiovascular autonomic function is essential for peak athletic performance. The aim of this study was to assess the effects of a Covid-19 disease on the autonomic nervous system of German elite athletes using heart rate variability (HRV). METHODS: 60 elite athletes (aged 22.88 +/- 4.71 years) were recruited, 30 of whom had undergone a Covid-19 disease. Heart rate (HR), blood pressure (BP) and heart rate variability (HRV) were measured during rest and during an orthostatic challenge. RESULTS: At rest and after orthostatic stress blood pressure and the root mean square of successive differences (RMSDD) were significantly lower in Covid-19 athletes (COV) than in control athletes (CON) (p = 0.002 and p = 0.004, respectively); heart rate was significantly higher (p = 0.001). COV showed a significantly greater reduction in blood pressure and elevation of heart rate than CON, but the change in RMSSD did not differ significantly during the orthostatic challenge. CONCLUSION: These results show a change in cardiac parasympathetic activity and cardiovascular autonomic function in German elite athletes after Covid-19. These findings further the understanding of effects of the Covid-19 disease on the cardiovascular physiology in athletes. Heart rate variability may be a helpful tool in the return-to-play assessment of elite athletes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11332-023-01067-7.