To elucidate the accuracy of benchmarks of criticality at the Kyoto University Critical Assembly (KUCA), uncertainty analysis is conducted for manufacturing tolerances in highly enriched uranium (HEU) plates and modeling of core configurations in addition to nuclear data. For evaluation of eigenvalue bias, eigenvalue calculations are conducted using MCNP6.1 and SCALE6.2/KENO-VI together with ENDF/B-VII.1. The modeling of reference core configurations and material properties with average values is validated through a comparison between calculated and measured results. The uncertainty induced by nuclear data is evaluated with SCALE6.2/TSUNAMI-3D together with ENDF/B-VII.1 for sensitivity calculations and 56groupcov.7.1 for the covariance matrix. In the breakdown of the uncertainty induced by nuclear data, the impact of 235U shows significant dominance, about 900 pcm in hard and soft spectrum cores. Furthermore, uncertainty evaluation by manufacturing tolerances in HEU plates and reproducibility of control rod positions demonstrates that the impact of variation on measured reactivity is minor. Through experimental analyses, the index of accuracy in benchmark experiments of criticality is conducive to the reliability of benchmarks at KUCA.