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A unified formulation for thermo-mechanical vibration analysis of size-dependent Timoshenko micro-beams comprised of functionally graded materials (FGMs) with general restraints is presented. The size effect is considered by incorporating the modified strain gradient theory into Timoshenko beam theory. The thermal and mechanical properties of FGMs are related to temperature and are assumed as continuous variation along the thickness. The Mori–Tanaka estimate is used for calculation of the material properties of FGM micro-beam. The formulation is deduced on the basis of the variational principle combined with penalty function method. The displacements and rotation of the FGM micro-beam are uniformly expanded by a modified Fourier series composed of traditional cosine series and some appropriate supplementary functions. Several comparisons of the present solutions with those from existing literature confirm the validity of the current formulation. In addition, a parametric study is given to demonstrate the influence of length scale parameters, gradient indices, end restraints and temperature changes on vibration characteristic of functionally graded micro-beam.