Diabetic foot ulcer (DFU) is a diabetic complication due to peripheral vasculopathy and neuropathy. A promising technology for wound healing in DFU is low-level light therapy (LLLT). Despite several studies showing positive effects of LLLT on DFU, LLLT’s physiological effects have not yet been studied. The objective of this study was to investigate vascular and nervous systems modification in DFU after LLLT. Two samples of 45 DFU patients and 11 healthy controls (HCs) were recruited. The total hemoglobin (totHb) concentration change was monitored before and after LLLT by near-infrared spectroscopy and analyzed in time and frequency domains. The spectral power of the totHb changes in the very-low frequency (VLF, 20 to 60 mHz) and low frequency (LF, 60 to 140 mHz) bandwidths was calculated. Data analysis revealed a mean increase of totHb concentration after LLLT in DFU patients, but not in HC. VLF/LF ratio decreased significantly after the LLLT period in DFU patients (indicating an increased activity of the autonomic nervous system), but not in HC. Eventually, different treatment intensities in LLLT therapy showed a different response in DFU. Overall, our results demonstrate that LLLT improves blood flow and autonomic nervous system regulation in DFU and the importance of light intensity in therapeutic protocols.