This study was performed to examine the quality of planning and treatment modality using a CyberKnife (CK) robotic radiosurgery system with multileaf collimator (MLC)-based plans and IRIS (variable aperture collimator system)-based plans in relation to the dose–response of secondary cancer risk (SCR) in patients with benign intracranial tumors. The study population consisted of 15 patients with benign intracranial lesions after curative treatment using a CyberKnife M6 robotic radiosurgery system. Each patient had a single tumor with a median volume of 6.43 cm3 (range, 0.33–29.72 cm3). The IRIS-based plan quality and MLC-based plan quality were evaluated by comparing the dosimetric indices, taking into account the planning target volume (PTV) coverage, the conformity index (CI), and the dose gradient (R10% and R50%). The dose–response SCR with sarcoma/carcinoma induction was calculated using the concept of the organ equivalent dose (OED). Analyses of sarcoma/carcinoma induction were performed using excess absolute risk (EAR) and various OED models of dose–response type/lifetime attributable risk (LAR). Moreover, analyses were performed using the BEIR VII model. PTV coverage using both IRIS-based plans and MLC-based plans was identical, although the CI values obtained using the MLC-based plans showed greater statistical significance. In comparison with the IRIS-based plans, the MLC-based plans showed better dose falloff for R10% and R50% evaluation. The estimated difference between Schneider’s model and BEIR VII in linear-no-threshold (Lnt) cumulative EAR was about twofold. The average values of LAR/EAR for carcinoma, for the IRIS-based plans, were 25% higher than those for the MLC-based plans using four SCR models; for sarcoma, they were 15% better in Schneider’s SCR models. MLC-based plans showed slightly better conformity, dose gradients, and SCR reduction. There was a slight increase in SCR with IRIS-based plans in comparison with MLC-based plans. EAR analyses did not show any significant difference between PTV and brainstem analyses, regardless of the tumor volume. Nevertheless, an increase in target volume led to an increase in the probability of SCR. EAR showed statistically significant differences in the soft tissue according to tumor volume (1–10 cc and ≥10 cc).