This study aimed to examine the agreement and acceptance of ultra-short-term heart rate (HR) variability (HRV(UST)) measures during post-exercise recovery in college football players. Twenty-five male college football players (age: 19.80 +/- 1.08 years) from the first division of national university championship voluntarily participated in the study. The participants completed both a repeated sprint ability test (RSA) and a Yo-Yo intermittent recovery test level 1 (YYIR1) in a randomized order and separated by 7 days. Electrocardiographic signals (ECG) were recorded in a supine position 10 min before and 30 min after the exercise protocols. The HR and HRV data were analyzed in the time segments of baseline 5~10 min (Baseline), post-exercise 0~5 min (Post 1), post-exercise 5~10 min (Post 2), and post-exercise 25~30 min (Post 3). The natural logarithm of the standard deviation of normal-to-normal intervals (LnSDNN), root mean square of successive normal-to-normal interval differences (LnRMSSD), and LnSDNN:LnRMSSD ratio was compared in the 1st min HRV(UST) and 5-min criterion (HRV(criterion)) of each time segment. The correlation of time-domain HRV variables to 5-min natural logarithm of low frequency power (LnLF) and high frequency power (LnHF), and LF:HF ratio were calculated. The results showed that the HRV(UST) of LnSDNN, LnRMSSD, and LnSDNN:LnRMSSD ratio showed trivial to small effect sizes (ES) (-0.00~0.49), very large and nearly perfect interclass correlation coefficients (ICC) (0.74~0.95), and relatively small values of bias (RSA: 0.01~-0.12; YYIR1: -0.01~-0.16) to the HRV(criterion) in both exercise protocols. In addition, the HRV(UST) of LnLF, LnHF, and LnLF:LnHF showed trivial to small ES (-0.04~-0.54), small to large ICC (-0.02~0.68), and relatively small values of bias (RSA: -0.02~0.65; YYIR1: 0.03~-0.23) to the HRV(criterion) in both exercise protocols. Lastly, the 1-min LnSDNN:LnRMSSD ratio was significantly correlated to the 5-min LnLF:LnHF ratio with moderate~high level (r = 0.43~0.72; p < 0.05) during 30-min post-exercise recovery. The post-exercise 1-min HRV assessment in LnSDNN, LnRMSSD, and LnSDNN:LnRMSSD ratio was acceptable and accurate in the RSA and YYIR1 tests, compared to the 5-min time segment of measurement. The moderate to high correlation coefficient of the HRV(UST) LnSDNN:LnRMSSD ratio to the HRV(criterion) LnLF:LnHF ratio indicated the capacity to facilitate the post-exercise shortening duration of HRV measurement after maximal anaerobic or aerobic shuttle running. Using ultra-short-term record of LnSDNN:LnRMSSD ratio as a surrogate for standard measure of LnLF:LnHF ratio after short-term bouts of maximal intensity field-based shuttle running is warranted.