Hypertrophic cardiomyopathy (HCM) is a common heritable cardiac disorder with diverse clinical outcomes including sudden death, heart failure, and stroke. Depressed heart rate variability (HRV), a measure of cardiac autonomic regulation, has been shown to predict mortality in patients with cardiovascular disease. Cardiac autonomic remodelling in animal models of HCM are not well characterised. We studied the Gly203Ser cardiac troponin‐I transgenic (TG) male mice previously demonstrated to develop hallmarks of HCM by age 21 weeks. 33 mice aged 30 and 50 weeks underwent continuous electrocardiogram (ECG) recording for 30 minutes under anesthesia. TG mice demonstrated prolonged P‐wave duration (p<0.001) and PR intervals (p<0.001) compared to controls. Additionally, TG mice demonstrated depressed standard deviation of RR intervals (SDRR; p<0.01), coefficient of variation of RR intervals (CVRR; p<0.001) and standard deviation of heart rate (SDHR; p<0.001) compared to controls. Additionally, total power was significantly reduced in TG mice (p<0.05). No significant age‐related difference in either strain was observed in ECG or HRV parameters. Mice with HCM developed slowed atrial and atrioventricular conduction and depressed HRV. These changes were conserved with increasing age. This finding may be indicative of atrial and ventricular hypertrophy or dysfunction, and perhaps an indication of worse clinical outcome in heart failure progression in HCM patients. This article is protected by copyright. All rights reserved.