BACKGROUND: Heart rate variability (HRV) is a marker of autonomic function. However, the reliability of short-term HRV measurement in individuals with combat-related traumatic injury (CRTI) remains undetermined. METHODS: An intra- and inter-rater reliability study was conducted using a subsample (n = 35) of British servicemen with CRTI enrolled in the ongoing ADVANCE study. A five-minute epoch of single-lead electrocardiogram data collected during spontaneous breathing was used to measure HRV. HRV analyses were independently performed by two examiners using Kubios. Intraclass correlation coefficient (ICC), standard error of measurement (SEM), minimum detectable change (MDC), and coefficient of variance were calculated for linear [root mean square of successive difference (RMSSD), standard deviation of NN interval, low-frequency, high-frequency, total power] and nonlinear (SD1-2, acceleration and deceleration capacities, sample entropy) measures. Bland-Altman %plots were used to assess bias in intra- and inter-rater HRV data. RESULTS: The mean age of participants was 39.3 ± 6.3 years. An excellent ICC score of 0.9998 (95% CI 0.9997, 0.9999) was observed for intra-rater analyses of RMSSD, and similar excellent ICC scores were seen for all other HRV measures. The inter-rater reliability analyses produced an excellent ICC score (range 0.97-1.00). Comparatively, frequency-domain measures produced higher MDC% and SEM% scores than time-domain and nonlinear measures in both inter- and intra-rater analyses. The Bland-Altman plots revealed relatively higher bias for frequency-domain and nonlinear measures than time-domain measures. CONCLUSION: ECG-related short-term HRV measures were reliable in injured servicemen under spontaneous breathing. However, the reliability appeared better with the time-domain measure than frequency-domain and nonlinear measures in this sample.