Uncertainty contribution on manufacturing factors and nuclear cross section in pebble bed nuclear fuel used in PBR250 of High Temperature Gas-cooled Reactor (HTGR) are quantified by the sampling method with the Monte Carlo within SCALE code system. The uncertainty quantification of various parameters embedded in PBR250 is under one of the framework of the IAEA Coordinate research project (CRP) on HTGR uncertainty analysis in modelling (UAM). Uncertainties of 17 manufacturing factors of pebble bed fuel are defined referring to ASTRA facility of Kurchatov institute in Russia, and correlations between manufacturing factors are considered according to manufacturing process of the pebble bed fuel. The SAMPLER module generates 1,000 sample inputs with perturbed input parameters given in KENO-VI input, and KENO-VI performs 1,000 Monte-Carlo simulations to obtain output distribution and its uncertainty which satisfies 95% confidence level with 4.2% upper and 4.6% lower limit of confidence interval. This paper describes the specification of the pebble bed model of IAEA UAM benchmark and presents uncertainty and sensitivity analysis (UA/SA) results on the effective multiplication factor due to manufacturing parameter uncertainties as well as cross section uncertainties. Uncertainty contribution due to manufacturing factor and cross section data to the effective multiplication factor is evaluated by 147 pcm and 707 pcm, respectively.