The technique of blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) was used to provide a spatial-temporal mapping of nociceptive activation in brain. We contrived to obtain an illustration of the pain related regions by injecting formalin at the hindpaw using a 4.7 T MR system in alpha-chloralose anesthetized rats. In order to obtain the pain response, we avoided any invasive surgery on animals to purify the signal of nociception. The dynamic data were analyzed by mapping correlation coefficient and the time activity curves were calculated by atlas-based region of interest selection. The BOLD signals showed obvious difference in anterior cingulated cortex, somatosensory cortex, medial thalamus, and striatum after stimulation. The results not only show the global somatotopic organization of noxious stimulation on hindpaw in rats, but also provided invaluable information for neuroscience research.