Introduction: COVID-19 pandemic primarily affected the respiratory system, but cardiovascular complications including autonomic dysfunction were increasingly recognized. Heart rate variability (HRV), a non-invasive measure of autonomic function, reflects the sympathovagal balance and provides an early warning of cytokine storms and impending cardiovascular complications. Aim: This study aimed to evaluate the relationship between COVID-19 clinical severity and HRV, and to examine the correlation between HRV and inflammatory markers. Methods: In this hospital-based case-control study 164 RT-PCR-confirmed COVID-19 patients and 43 age and gender-matched healthy controls participated in the study. Their clinical profiles, inflammatory markers were noted on admission and their HRV parameters (time and frequency domains) were evaluated using 5-minute ambulatory ECG recordings. Logistic regression was used to assess associations between HRV and clinical severity; ANOVA was used for post hoc comparisons across groups. Results: Among the 164 COVID-19 patients, 44% had mild or no symptoms, while 56% had moderate to severe infection. Co morbid conditions were present in 62.8%, with diabetes being the most common (43.9%). HRV parameters—including HF, LF, LF/HF ratio, and PNN50 were significantly associated with disease severity in both logistic regression models (p < 0.05). Weak correlations were observed between HRV (SDNN) and inflammatory markers such as D-Dimer, LDH, IL-6, and CRP. Conclusion: This study confirmed the presence of autonomic dysfunction in COVID-19 patients, with more pronounced dysfunction observed in those with greater clinical severity. Heart rate variability serve as a valuable early indicator of COVID-19 severity and progression