A number of previous studies of acupuncture acupoint specificity have used sham acupoints, sham acupuncture or meridian acupoints at a great distance from each other as controls in functional MRI (fMRI) experiments. However, few studies have compared different meridian acupoints within the same segment, which are associated with similarly intense needle sensations. We performed fMRI on 12 healthy young volunteers and observed differences in brain activation elicited by acupuncture of the Taixi (KI 3) and Qiuxu (GB 40) acupoints. Acupuncture was applied at the Taixi and Qiuxu acupoints, using a multiple-block fMRI design with three blocks, involving three alternations of resting and task phases. After scanning, needle sensation was assessed. The behavioral results revealed that the subjective needle sensation was similar between the Taixi and Qiuxu acupoints. The fMRI results revealed that acupuncture at the right Taixi acupoint activated the right superior temporal gyrus (BA 22), left middle frontal gyrus (BA 46) and inferior frontal gyrus (BA 45), bilateral parietal lobe postcentral gyrus (BA 2), right parietal lobe (BA 3), and left parietal lobe (BA 40). Acupuncture at the right Qiuxu acupoint activated the left superior temporal gyrus (BA 42), right parietal lobe postcentral gyrus (BA 40, BA 43), right inferior frontal gyrus (BA 47), bilateral superior temporal gyrus (BA 22), and right insula BA13. These results suggest that the right Taixi and Qiuxu acupoints activated different brain areas.