Performances of radiosurgery of intracranial lesions between cone-based Linac system and Tomotherapy-based system were compared in terms of dosimetry and time. Twelve patients with single intracranial lesion treated with cone-based Linac radiosurgery system from 2005 to 2009 were replanned for Tomotherapy-based radiosurgery treatment. The conformity index, homogeneity index (HI), and gradient score index (GSI) of each case was calculated. The Wilcoxon matched-pair test was used to compare the 3 indices between both systems. The cases with regular target (n = 6) and those with irregular target (n = 6) were further analyzed separately. The estimated treatment time between both systems was also compared. Significant differences were found in HI (p = 0.05) and in GSI (p = 0.03) for the whole group. Cone-based radiosurgery was better in GSI whereas Tomotherapy-based radiosurgery was better in HI. Cone-based radiosurgery was better in conformity index (p = 0.03) and GSI (p = 0.03) for regular targets, whereas Tomotherapy-based radiosurgery system performed significantly better in HI (p = 0.03) for irregular targets. The estimated total treatment time for Tomotherapy-based radiosurgery ranged from 24 minutes to 35 minutes, including 15 minutes of pretreatment megavoltage computed tomography (MVCT) and image registration, whereas that for cone-based radiosurgery ranged from 15 minutes for 1 isocenter to 75 minutes for 5 isocenters. As a rule of thumb, Tomotherapy-based radiosurgery system should be the first-line treatment for irregular lesions because of better dose homogeneity and shorter treatment time. Cone-based Linac radiosurgery system should be the treatment of choice for regular targets because of the better dose conformity, rapid dose fall-off, and reasonable treatment time.