There is limited literature on the ability of high-frequency cerebral functional near-infrared spectroscopy (fNIRS) systems to characterize cerebral autoregulation/cerebrovascular reactivity (CA/CVR) regional disparity than other low-frequency commercial systems. To overcome temporal and spatial limitations of existing commercial NIRS systems, we created a custom-built whole brain CVR mapping system using fNIRS. We preliminarily evaluated regional hemispheric disparity in CA/CVR using various fNIRS derived metrics based on relative hemoglobin concentrations. Healthy volunteer data was recorded for approximately 90 minutes in a block-trial fashion with baseline and perturbation testing. Five types of hemoglobin-based indices were derived using 1 Hz and 250 Hz sampled data. Regional hemispheric disparity between brain lobar regions was evaluated based on median and median absolute deviation metrics. Multi-variate cerebral physiologic relationships between hemispheres were assessed via optimal autoregressive integrative moving average (ARIMA), vector ARIMA impulse response functions, and Granger causality analyses. Data from 50 healthy control volunteers were prospectively analyzed. Our system was able to detect subtle differences between corresponding right and left brain regions through all statistical methods employed, demonstrating the ability of our novel system to detect changes in regional variation of fNIRS and derived CVR measures. These were present and magnified during perturbation testing compared to baseline recordings. However, given the healthy nature of the study population, large differences in CVR measures between brain regions and extreme CVR derangements were not seen. Our custom built fNIRS whole brain CVR mapping system was able to detect subtle regional differences in CVR measures across various time-domain analytic techniques. These findings are in alignment with prior literature, supporting the notion that research-grade fNIRS systems may be adequate for regional disparity analysis of CVR in humans. Future work in diseased/injured human cohorts is required to further quantify the sensitivity of our custom-built system to detect regional variations and disturbances in CVR.