Whether morning heart rate variability (HRV) predicts the magnitude of its circadian variation in the absence of disease or is influenced by chronotype is unclear. We aimed to quantify associations between (1) morning HRV and its diurnal change, and (2) morning HRV and a Morningness–Eveningness Questionnaire (MEQ)-derived chronotype. Resting electrocardiograms were obtained in the morning and evening on separate days in a counterbalanced order to determine the mean RR interval, root mean square of successive differences (RMSSD), and standard deviation of normal-to-normal RR intervals (SDNN) in 23 healthy men (24.6 ± 3.4 yrs; body mass index: 25.3 ± 2.8 kg/m2). The MEQ was completed during the first laboratory visit. Morning RMSSD and SDNN were significantly higher (Ps < 0.05) than evening values. Morning RMSSD and SDNN were associated with their absolute (Ps < 0.0001), and relative diurnal changes (Ps < 0.01). No associations were observed between HRV parameters and the MEQ chronotypes (Ps > 0.09). Morning HRV was a stronger determinant of its evening change than chronotype. Greater diurnal variation in HRV was dependent on higher morning values. Strategies to improve basal HRV may therefore support healthier cardio-autonomic circadian profiles in healthy young men.