Background: Hypertension remains a life-threatening risk factor for cardiovascular diseases globally. It is not only common to middle age or aged group but also affect young individuals. Heart rate variability (HRV) gives an inference of the overall cardiac function and health of an individual. Thus, the aim of this study was to investigate whether HRV could be an early marker and a valid alternative to biochemical probes for the early detection of cardiac injury and systemic inflammation in hypertensive young adults. Materials and methods: A total number of 300 participants were recruited by fixed sampling of the case control study grouped into normotensive and hypertensive young groups. Informed consent was obtained from all participants before the procedure. Blood pressure with some anthropometric data were collected. Afterward, each participant’s HRV data was acquired by conducting a 5-minute resting ECG. Then, 5 ml of blood was taken through sterile venepuncture, centrifuged at 3000 rpm for 15 mins and biochemical analysis was performed for plasma troponin-I, troponin-T and inflammatory markers (TNF-alpha and NF-kappaB). Results: HRV assessment showed significant decrease in HRV parameters of parasympathetic activity (SDNN, RMSSD, HF) in the hypertensive young group. LF also showed significant decrease in the hypertensive group. But, LF/HF (sympatho-vagal balance) showed significant increase in the hypertensive group. LF correlates with plasma TNF-α (r = -0.6167) and NF-kB (r = -0.6673) at p = 0.0003 and p<0.0001, respectively. In addition, LF correlates with plasma Troponin-I (r = -0.6393) and Troponin-T (r = -0.5719) at p = 0.0001 and p = 0.0010, respectively. LF/HF had no correlation with these biomarkers. Thus, HRV correlates with plasma troponin-I, troponin-T, TNF-alpha and NF-kappaB in hypertensive young adults. Conclusion: HRV can be used as an early marker of cardiac injury and inflammation in young hypertensive individuals.