The technological and financial limitations in the manufacturing process are the reason for non-achievability of nominal dimension. Therefore, tolerance allocation is of significant importance for assembly. Conventional tolerance allocation methods are limited by an assumption that all parts are rigid. Every mechanical assembly consists of at least one or more flexible parts which undergo significant deformation due to inertia effect. Finite element analysis is used to determine the deformation of components in an assembly. Therefore, integration of statistical tolerance design with finite element analysis will guarantee that the optimal tolerance values of various components of the assembly obtained as end product of the tolerance design will remain within tolerance variation. Then the product can function as intended under a wide range of operating conditions for the duration of its life. In this paper, tolerance design of a piston cylinder assembly is done to demonstrate the proposed methodology.