The paper presents state space models of the hemodynamic response (HR) of fNIRS to an impulse stimulus in three brain regions: motor cortex (MC), somatosensory cortex (SC), and visual cortex (VC). Nineteen healthy subjects were examined. For each cortex, three impulse HRs experimentally obtained were averaged. The averaged signal was converted to a state space equation by using the subspace method. The activation peak and the undershoot peak of the oxy-hemoglobin (HbO) in MC are noticeably higher than those in SC and VC. The time-to-peaks of the HbO in three brain regions are almost the same (about 6.76 76 ± 0.2 s). The time to undershoot peak in VC is the largest among three. The HbO decreases in the early stage (~0.46 s) in MC and VC, but it is not so in SC. These findings were well described with the developed state space equations. Another advantage of the proposed method is its easy applicability in generating the expected HR to arbitrary stimuli in an online (or real-time) imaging. Experimental results are demonstrated.