The present study reported the development of a novel functional photoacoustic microscopy (fPAM) system for investigating hemodynamic changes in rat cortical vessels associated with electrical forepaw stimulation. Imaging of blood optical absorption by fPAM at multiple appropriately-selected and distinct wavelengths can be used to probe changes in total hemoglobin concentration (HbT, i.e., cerebral blood volume [CBV]) and hemoglobin oxygen saturation (SO2). Changes in CBV were measured by images acquired at a wavelength of 570 nm (λ570), an isosbestic point of the molar extinction spectra of oxy- and deoxy-hemoglobin, whereas SO2 changes were sensed by pixel-wise normalization of images acquired at λ560 or λ600 to those at λ570. We demonstrated the capacity of the fPAM system to image and quantify significant contralateral changes in both SO2 and CBV driven by electrical forepaw stimulation. The fPAM system complements existing imaging techniques, with the potential to serve as a favorable tool for explicitly studying brain hemodynamics in animal models.