This study evaluated the dose calculation accuracy of a Monte Carlo (MC)-based independent dose calculation system (IDCS) for CyberKnife brain stereotactic treatment plans and compared it with ray-tracing (RT) and MC algorithms within the MultiPlan treatment planning system (TPS). Beam modeling accuracy was validated for 11 circular fields using measured output factors (OPF), percentage depth dose (PDD), and off-center ratio (OCR). A total of 200 retrospective brain stereotactic treatment plans were analyzed (50 prescribed 23 Gy in 1 fraction, 50 prescribed 35 Gy in 3 fractions, and 100 prescribed 41.5 Gy in 5 fractions). Among these, 24 quality assurance (QA) plans were evaluated using homogeneous cylindrical phantoms and ionization chambers. Dose-volume histogram (DVH) was calculated, and gamma analysis (3%/1 mm, 10% threshold) was performed. IDCS aligned with measured data, with OPF and PDD/OCR errors within 3% and 4%, respectively, except for small-field underestimations in the build-up region. For QA plans, TPS overestimated the measured dose (RT: 0.5% ± 2.6%, p = 0.58, MC: 1.7% ± 3.1%, p = 0.07), while IDCS underestimated it (- 1.3% ± 2.3%, p = 0.07). Gamma passing rates were 98.9% ± 1.5% (TPS-RT vs. IDCS) and 99.9% ± 0.3% (TPS-MC vs. IDCS). DVH metrics (planning target volume [PTV]: D98%, D95%, and D2%) showed clinically acceptable differences. IDCS showed greater dose calculation accuracy than the TPS-RT algorithm and could identify dose discrepancies in specific cases, thereby confirming its reliability for CyberKnife QA.