Background: Heart rate variability (HRV) analysis computed on R-R interval series of ECG records with heavy burden of ectopic beats or non-sinus rhythm can significantly distort HRV parameters and hence clinically ineligible for HRV analysis. Yet, existing algorithmic methods of HRV analysis do not check such eligibility and require manual identification of eligible window (portion of ECG record) to ensure reliability. Objective: We aimed to propose a robust algorithm with a sliding window feature to automate the identification of an eligible window, if available, which compute HRV parameters within that window obviating manual input. Methods: The proposed algorithm classifies each window as either eligible or ineligible. With a window classified eligible, we stop sliding through the record, otherwise we move to the next window and repeat the eligibility identification process, until either an eligible window is found, or all windows are exhausted. Results: When evaluated on random subset of 100 records from MIMIC-III waveform database, the proposed algorithm excluded every ineligible record, and missed only 1.25% of eligible ones. The HRV parameters computed using proposed method closely approximated the standard HRV analysis with Pearson correlation coefficients (ideally one) and fractions of variance unexplained (ideally zero) ranging from 96.3% to 99.8% and 0.34% to 7.43%, respectively. Conclusions: When translated into practice, proposed algorithm will reduce clinicians'' burden without compromising the accuracy of HRV analysis, potentially leading to its wider adoption. © 2023 Elsevier Inc.