Measures reflecting cardiac sympathovagal activity, particularly those associated with heart rate variability (HRV), are widely recognized and utilized in both scientific and clinical contexts. This study aimed to assess the inter- and intra-examiner reliability of short-term HRV parameters in patients hospitalized with coronavirus disease 2019 (COVID-19). A total of 103 patients (both sexes) diagnosed with COVID-19 were included in the study. HRV was analyzed using both linear and nonlinear methods. Reliability was evaluated through intraclass correlation coefficient (ICC2.1), minimum detectable change (MDC), standard error of measurement (SEM), and coefficient of variation (CV). According to Fleiss’ criteria, excellent reliability was demonstrated, with ICC values ranging from 0.970 to 0.999 for Examiner 1, and from 0.956 to 0.999, for Examiner 2. In the inter-examiner analysis, the ICCs of HRV parameters ranged from 0.972 to 0.999. SEM values for intra-examiner reliability for Examiner 1 ranged from 0.02 to 5.64, with MDC values from 0.05 to 15.64, and CV (%) from 0.28 to 8.04. For Examiner 2, SEM values ranged from 0.02 to 8.18, MDC values from 0.05 to 22.68, and CV (%) from 0.24 to 8.14. For inter-examiner reliability, SEM values ranged from 0.02 to 6.17, MDC from 0.06 to 17.11, and CV (%) from 0.34 to 9.81. Across all analyses, CVs for HRV parameters remained below 10%. Considering different time points and different examiners, short-term resting HRV measurements in patients hospitalized with COVID-19, as evaluated using a portable heart rate device, exhibit high reliability.