Practical mechanical systems often contain several flexible components and uncertain parameters which makes it hard to predict the system behavior and performance exactly. This research presents the uncertainty analysis of flexible multibody systems with random variables. Absolute nodal coordinate formulation (ANCF), which is different from the traditional finite element method, is employed to model the flexibility here. Monte Carlo method is successfully used to simulate flexible multibody systems of index-3. The method proposed is demonstrated by an example of flexible slider-crank mechanism.