Background Tumor involving the septum pellucidum is uncommon. Surgery as the main therapeutic procedure for this lesion is a challenge to neurosurgeons. We analyzed the clinical characteristics and pathological features of septum pellucidum tumor in 41 patients and compared the curative effects of frontal transcortical, trans-sulcal and interhemispheric transcallosal approaches. Methods Clinical characteristics and the pathological features of septum pellucidum tumor were investigated retrospectively in 41 patients. The differences in postoperative residual rates, extents of tumors and resection of normal brain tissues after use of the three approaches in these patients were analyzed statistically. Results Septum pellucidum tumor is more likely to attack young or middle-aged persons. The tumor mainly presents itself as a central neurocytoma or cerebral low-grade glioma in pathology and manifests as intracranial hypertension clinically. No difference was found in the extent of tumor resection but significant difference in the extent of normal brain tissue resection and in postoperative disability rate among the three approaches. The transcortical approach brought about the most serious injury to brain tissue and the highest disability rate, Whereas the frontal transcallosal approach the lightest injury and the lowest disability rate. The injury to brain tissue and the disability rate brought about by the front trans-sulcus approach were between the above two approaches. Conclusions Operation is still regarded the major treatment for septum pellucidum tumor. Transcallosal and trans-sulcus approaches are fit with the concept of minimally invasive surgery, and transcallosal approach is the first choice for septum pellucidum tumor.