Physical fatigue can be assessed using heart rate variability (HRV). We measured HRV at rest and in a fatigued state using impulse-radio ultra wideband (IR-UWB) radar in a noncontact fashion and compared the measurements with those obtained using electrocardiography (ECG) to assess the reliability and validity of the radar measurements. HRV was measured in 15 subjects using radar and ECG simultaneously before (rest for 10 min before exercise) and after a 20-min exercise session (fatigue level 1 for 0–9 min; fatigue level 2 for 10–19 min; recovery for ≥ 20 min after exercise). HRV was analysed in the frequency domain, including the low-frequency component (LF), high-frequency component (HF) and LF/HF ratio. The LF/HF ratio measured using radar highly agreed with that measured using ECG during rest (ICC = 0.807), fatigue-1 (ICC = 0.712), fatigue-2 (ICC = 0.741) and recovery (ICC = 0.764) in analyses using intraclass correlation coefficients (ICCs). The change pattern in the LH/HF ratios during the experiment was similar between radar and ECG. The subject’s body fat percentage was linearly associated with the time to recovery from physical fatigue (R2 = 0.96, p < 0.001). Our results demonstrated that fatigue and rest states can be distinguished accurately based on HRV measurements using IR-UWB radar in a noncontact fashion.