This study compared the efficacy of CT-on-rails versus in-room CBCT for daily adaptive proton therapy. CT-on-rails provides high precision accuracies, but the increased treatment execution uncertainties may affect the adaptation efficacy, which include 1) isocenter matching since the patient is not imaged in the treatment position, but either “near-treatment-position” imaging; 2) random patient movements induced by the couch motion. A cohort of ten head-and-neck patients with daily CBCT and corresponding virtual CT images were used for analysis where DVH metrics were evaluated for all regions of interest and on-line adaptation were compared. The findings of this study show that the extra uncertainties associated with the use of CT-on-rails do not affect dosimetric adaptation efficacy if the uncertainty due to couch motion-induced patient’s movement does not exceed 2 mm, and the isocenter-matching uncertainty is below 1 mm. This study concluded that there is no clinically significant dosimetric difference between CBCT and in-room CT-on-rails for online adaptive therapy of head-and-neck patients. Therefore, in-room CT-on-rails can be considered a good alternative to CBCT for adaptive proton therapy.