The total system error (TSE) of a CyberKnife® system was measured using two phantom-based methods and one patient-based method. The standard radiochromic film (RCF) end-to-end (E2E) test using an anthropomorphic head and neck phantom and isocentric treatment delivery was used with the 6Dskull, Fiducial and Xsight® spine (XST) tracking methods. More than 200 RCF-based E2E results covering the period from installation in 2006 until 2017 were analyzed with respect to tracking method, system hardware and software versions, secondary collimation system, and years since installation. An independent polymer gel E2E method was also applied, involving a 3D printed head phantom and multiple spherical target volumes widely distributed within the brain. Finally, the TSE was assessed by comparing the delineated target in the planning computed tomography images of a patient treated for a thalamic functional target with the radiation-induced lesion defined on the six-month follow-up magnetic resonance (MR) images. Statistical analysis of the RCF-based TSE results showed mean ± standard deviation values of 0.40 ± 0.18 mm, 0.40 ± 0.19 mm, and 0.55 ± 0.20 mm for the 6Dskull, Fiducial, and XST tracking methods, respectively. Polymer gel TSE values smaller than 0.66 mm were found for seven targets distributed within the brain, showing that the targeting accuracy of the system is sustained even for targets situated up to 80 mm away from the center of the skull. An average clinical TSE value of 0.87 ± 0.25 mm was also measured using the FSE T2 and FLAIR post-treatment MR image data. Analysis of the long-term RCF-based E2E tests showed no changes of TSE over time. This study is the first to report long-term (>10 years) analysis of TSE, TSE measurement for targets positioned at large distances from the virtual machine isocenter, or a clinical assessment of TSE for the CyberKnife system. All of these measurements demonstrate TSE consistently < 1 mm.