Pulse rate variability (PRV) can be extracted from functional near-infrared spectroscopy (fNIRS) (PRVNIRS) and photoplethysmography (PPG) (PRVPPG) signals. The present study compared the accuracy of simultaneously acquired PRVNIRS and PRVPPG, and evaluated their different characterizations of the sympathetic (SNS) and parasympathetic (PSNS) autonomous nervous system activity. Ten healthy subjects were recorded during resting-state (RS) and respiratory challenges in two temperature conditions, i.e., room temperature (23°C) and cold temperature (4°C). PRVNIRS was recorded based on fNIRS measurement on the head, whereas PRVPPG was determined based on PPG measured at the finger. Accuracy between PRVNIRS and PRVPPG, as assessed by cross-covariance and cross-sample entropy, demonstrated a high degree of correlation (r<0.9), which was significantly reduced by respiration and cold temperature. Characterization of SNS and PSNS using frequency-domain, time-domain, and nonlinear methods showed that PRVNIRS provided significantly better information on increasing PSNS activity in response to respiration and cold temperature than PRVPPG. The findings show that PRVNIRS may outperform PRVPPG under conditions in which respiration and temperature changes are present, and may, therefore, be advantageous in research and clinical settings, especially if characterization of the autonomous nervous system is desired.