This paper demonstrated the free vibration of a planar two-link flexible manipulator with harmonic drivers and non-uniformity in the cross-section of links. A dynamic model has been developed that incorporates flexibilities in both link and joint experiencing harmonic vibration, with joint flexibility modeled as torsional spring-inertia components combination. Two links were modeled based on Von Karman’s nonlinear strain relations and theory of the Euler-Bernoulli beam. The nonlinear governing equations were derived using the extended Hamilton’s principle for planar two-link flexible manipulators with variable cross-sections for each link. The coefficients of the obtained partial differential equations were as a function of spatial coordinates and were reduced to the ordinary differential equations for a family of cross-section geometries with exponentially varying widths of rectangular sections of each link. The frequency equation was obtained and analytical solutions of the vibration were achieved for different exponential shapes of each link (widening and narrowing beam for each link). Natural frequencies and mode shapes were presented for varying cross-section areas of the links. The effects of the end masses, payload, beam mass density, flexural rigidity ratio, and joint frequency were investigated on the mode shapes and natural frequencies when the power of the exponential function of the cross-sectional areas of two links was varied. The numerical results were verified with experimental results.