A 67-year-old woman presented for evaluation of severe coccygeal pain. The computed tomography scans and magnetic resonance imaging showed an asymmetric midline sacral tumor invading the right lower portion of S2. To preserve both S2 nerve roots and to obtain negative surgical margins, a modified mid-sacrectomy with an aid of a computed navigation system was performed. The sacral tumor was excised en bloc with negative tumor margins. Both S2 nerve roots were preserved and additional reconstruction was not necessary because of minimal resection of the sacroiliac joint. We report a case of a sacral chordoma which was excised en bloc with adequate surgical margins by a computer-assisted modified mid-sacrectomy. The computed navigation system may be a useful tool for tumor targeting and safe osteotomies in sacral tumor surgery via the posterior only approach.