Industrial applications of computed tomography (CT) for dimensional metrology on various components are fast increasing, owing to a number of favorable properties such as capability of non-destructive internal measurements. Uncertainty evaluation is however more complex than in conventional measurement processes, e.g., with tactile systems, also due to factors related to systematic errors, mainly caused by specific CT image characteristics. In this paper we propose a simulation-based framework for measurement uncertainty evaluation in dimensional CT using the bootstrap method. In a case study the problem concerning measurement uncertainties was addressed with bootstrap and successfully applied to ball-bar CT measurements. Results obtained enabled extension to more complex shapes such as actual industrial components as we show by tests on a hollow cylinder workpiece.