The effects of a cutout and thermal environment on the three-dimensional vibration characteristics of functionally graded cylindrical micropanels with different boundary conditions are investigated. The micropanel material properties are assumed temperature dependent and graded in the thickness direction. The motion equations are based on the modified couple stress theory in combination with the three-dimensional elasticity theory. The frequency equations are derived using the Chebyshev–Ritz method. The multiple boundary conditions are implemented by suitably choosing the Ritz basis functions. The reliability and accuracy of the results are confirmed by comparing them with available solutions in the open literature. Finally, the effects of material length scale parameter, material gradient index, thickness-to-mean radius ratio, cutout length to micropanel length ratio, temperature rise and boundary conditions on the natural frequencies of the micropanels are carried out and discussed.