The purpose of this study was to determine the relationship between smartphone-derived heart rate measures (resting heart rate [RHR] and heart rate variability [HRV]) and performance on an aerobic performance test. Seventeen male college students performed 55-second HR measures in the seated position every morning for 5 days. The root mean square of successive normal-to-normal interval differences (RMSSD) was used as the HRV metric. The weekly mean and coefficient of variation of RHR (RHRM and RHRCV, respectively) and RMSSD (RMSSDM and RMSSDCV, respectively) were determined. Participants completed the 2 mile run (2MR) on the last day of the week. Intra-class correlations (ICC) were used to determine the stability in the heart rate measures across the 5-day period. Pearson correlations were performed to determine the relationship between 2MR and RHRCV, HRM, RMSSDM and RMSSDCV. RHR (ICC = 0.87 [0.74 to 0.95], p < 0.05) displayed better stability over the 5-day period relative to the RMSSD (ICC = 0.66 [0.32 to 0.86], p < 0.05). RHRM was very strongly correlated with 2MR (r = 0.63), as was RMSSDCV (r = 0.55). Conversely, neither RHRCV nor RMSSDM correlated significantly to the 2MR. Therefore, both RHRM and RMSSDCV may be useful objective heart rate indicators to reflect aerobic performance.