Abstract: This paper describes a framework for stochastic dynamic analysis and reliability assessment of large aqueduct structures that combines the continuum damage mechanics of concrete and the probability density evolution theory to model random ground motions using a refined FEM procedure. This new approach adopts a fiber beam element in OpenSEES to simulate the three-dimensional behaviors of the reinforced concrete structure of a prototype aqueduct, and generates one hundred samples of random ground motions with assigned probabilities using a physical random function model. We make a stochastic dynamic analysis obtaining the random dynamic responses of this structure and then adopt a probability density evolution method to examine the effect of random fluctuations in the responses. Dynamic reliability curves at different failure thresholds can be obtained for large aqueduct structures that are given absorbing boundary conditions associated with the ultimate displacement ratios of the piers. Thus, the framework and analysis in this study is a useful tool for seismic analysis and reliability design of large aqueduct structures.