Background: To compare thermoplastic masks (TMP) and vacuum cushion system (VCS) to assess differences in interfraction set up accuracy in patients treated with stereotactic radiotherapy (SBRT) for oligometastatic lung cancer. Secondarily, to survey radiotherapy technologists to assess their satisfaction with the two systems. Methods: Retrospective study of patients treated with lung SBRT between 2008 to 2012 at our institution. Immobilization was performed for 73 treatment sessions (VCS = 40; TMP = 33). A total of 246 cone-beams were analysed. Patients considered ineligible for surgery with a life expectancy ≥6 months and performance status > 1 were included. Target lesion location was verified by cone beam computed tomography (CBCT) prior to each session, with displacements assessed by CBCT simulation prior to each treatment session. Couch shifts were registered prospectively in vertical, longitudinal, and latero-lateral directions to obtain Kernel coordinates (3D representation). Technologists were surveyed to assess their satisfaction with indexing, positioning, and learning curve of the two systems. Setup displacements were obtained in all patients for each treatment plan and for each session. To assess differences between the immobilization systems, a t-test (Welch) was performed. Results: Mean displacements for the TMP and VC systems, respectively, were as follows: session one, 0.64 cm vs 1.05 cm (p = 0.0002); session two, 0.49 cm vs 1.02 cm (p < 0.0001), and session three, 0.56 vs 0.97 cm (p = 0.0011). TMP resulted in significantly smaller shifts vs. VCS in all three treatment sessions. Technologists rated the learning curve, set up, and positioning more highly for TMP versus VCS. Conclusions: Due to the high doses and steep gradients in lung SBRT, accurate and reproducible inter-fraction set up is essential. We found that thermoplastic masks offers better reproducibility with significantly less interfractional set up displacement than vacuum cushions. Moreover, radiotherapy technologists rated the TMP system higher. Taken together, these two findings suggest that TMP may be preferable to VCS. However, more research is needed to determine both inter- and intrafraction error to identify the optimal immobilisation system for use in lung SBRT.