Generalized orthogonal polynomials which include all types of orthogonal polynomial are introduced first. Using the idea of orthogonal polynomials that can be expressed by a Taylor power series and vice versa, the operational matrix for the integration of the generalized orthogonal polynomials is first derived. A stretched operational matrix of diagonal form is also derived. Both the operational matrix for the integration and the stretched operational matrix of generalized orthogonal polynomials are applied to solve functional differential equations. The characteristics of each kind of orthogonal polynomial in solving the scaled system is demonstrated. The computational strategy for finding the expansion coefficients of the state variables is very simple, straightforward and easy. The inversion of only one matrix, which has the same dimension as the state variables, is required. The expansion coefficients of the state variables are obtained by the proposed recursive formula. Much computer time is thus saved and computational results are obtained that are very accurate compared with previous methods.