Abstract Background Equine asthma in severe form (severe equine asthma [sEA]) shares remarkable similarities with human asthma. Human studies detected changes in the autonomic nervous system function in asthmatic patients based on heart rate variability (HRV) analysis. Study design Observational study. Objectives To investigate the relationship between sEA and HRV in horses. Methods Twenty horses diagnosed with sEA and 20 asymptomatic (non‐sEA) horses were investigated. SEA horses showed clinical signs. The RR intervals of the ECG were recorded for 1 h at rest between 9 AM and 11 AM using a heart rate (HR) monitor. HRV data were calculated using Kubios software. Parameters recorded for the sEA and non‐sEA groups were compared using one‐way MANOVA model. The significance level was set at α = 0.05. Results SD2 (mean 99.6 ± SD 25.3 vs. 42.5 ± 17.1), SDNN (82.7 ± 20.7 vs. 41.3 ± 14.3), TINN (398.1 ± 104.9 vs. 209.3 ± 71.9), SD2/SD1 ratio (1.7 ± 0.2 vs. 1.1 ± 0.3), Total power (4740.2 ± 1977.9 vs. 1503.0 ± 1179.3), LF (2415.3 ± 1072.4 vs. 707.4 ± 649.9), SD1 (60.9 ± 15.9 vs. 39.2 ± 14.1), RMSSD (86.0 ± 22.6 vs. 55.3 ± 19.8) and HF (1575.8 ± 902.5 vs. 578.1 ± 491.1) were lower in sEA horses compared with the non‐sEA horses ( p < 0.01 for each variable). SD2, SDNN, TNN, the SD2/SD1 ratio and Total power showed the greatest discriminatory power in differentiating the sEA and non‐sEA groups. Main limitations Small sample size. Conclusion Our findings indicate that like humans, asthmatic horses show an overall reduction in autonomic control. A relative increase of the parasympathetic modulation of the heart was also observed. After further investigations, HRV measurement might be a non‐invasive approach to monitor autonomic nervous system responses of sEA horses.