In this paper, we extend our previous work on the dynamic buckling analysis of isogeometric shell structures to the stochastic situation where an isogeometric deterministic dynamic buckling analysis method is combined with spectral-based stochastic modeling of geometric imperfections. To be specific, a modified Generalized-α time integration scheme combined with a nonlinear isogeometric Kirchhoff–Love shell element is used to simulate the buckling and post-buckling problems of cylindrical shell structures. Additionally, geometric imperfections are constructed based on NURBS surface fitting, which can be naturally incorporated into the isogeometric analysis framework due to its seamless CAD/CAE integration feature. For stochastic analysis, the method of separation is adopted to model the stochastic geometric imperfections of cylindrical shells based on a set of measurements. We tested the accuracy and convergence properties of the proposed method with a cylindrical shell example, where measured geometric imperfections were incorporated. The ABAQUS reference solutions are also presented to demonstrate the superiority of the inherited smooth and high-order continuous properties of the isogeometric approach. For stochastic dynamic buckling analysis, we evaluated the buckling load variability and reliability functions of the cylindrical shell with 500 samples generated based on seven nominally identical shells reported in the geometric imperfection data bank. It is noted that the buckling load variability in the cylindrical shell obtained with static nonlinear analysis is also presented to show the differences between dynamic and static buckling analysis.