The stochastic analysis of composite structures with partially restrained (PR) connections under seismic loads present some interesting and challenging issues to practicing engineers. This paper proposes an efficient, robust, and accurate method for stochastic finite element analysis of concrete–steel composite structures allowing for PR connections. These are followed by suitable numerical example which indicates that employment of such a stochastic finite element analysis. The Kocaeli earthquake in 1999 is considered as a ground motion. The connections parameters and material properties are random variables. It is essential to properly consider the PR connections in the stochastic dynamic analysis and design of the steel-concrete composite structures since design forces change significantly. The assumption that the connections are rigid, which is routinely used in the application, is not proper. The effect of the variability connection stiffness on the composite structures responses is sufficiently important for consideration in structural safety.