The purpose of this study was to evaluate the agreement of the vagal-related heart rate variability index, log-transformed root mean square of successive R-R intervals (lnRMSSD), measured under ultra-short-term conditions (< 60 seconds) with conventional longer term recordings of 5 minutes in collegiate athletes under resting and post-exercise conditions. Electrocardiographic readings were collected from twenty-three athletes within 5-minute segments at rest and at 25-30 minutes of supine recovery following a maximal exercise test. From each 5-minute segment, lnRMSSD was recorded as the criterion measure. Within each 5-minute segment, lnRMSSD was also determined from randomly selected ultra-short-term segments of 10-, 30-, and 60-seconds in length, which were compared to the criterion. When compared to the criterion measures, the significant intraclass correlation (from 0.98 to 0.81, p < 0.05) and typical error (from 0.11 to 0.34) increased as ultra-short-term measurement duration decreased (i.e., from 60 seconds to 10 seconds). In addition, the limits of agreement (Bias ± 1.98 SD) increased as ultra-short-term lnRMSSD duration decreased as follows: 0.00 ± 0.22 ms, -0.07 ± 0.41 ms, -0.20 ± 0.94 ms for the 60-, 30-, and 10-second pre-exercise segments, respectively, and -0.15 ± 0.39 ms, -0.14 ± 0.53 ms, -0.12 ± 0.76 ms for the 60-, 30-, and 10-second post-exercise segments, respectively. This study demonstrated that as ultra-short-term measurement duration decreased from 60 seconds to 10 seconds, the agreement to the criterion decreased. Therefore, 60 seconds appears to be an acceptable recording time for lnRMSSD data collection in collegiate athletes.