Abstract The present work aims to analyze the natural and whirl frequencies of a slant-cracked functionally graded rotor-bearing system using finite element analysis for the flexural vibrations. The functionally graded shaft is modelled using two nodded beam elements formulated using the Timoshenko beam theory. The flexibility matrix of a slant-cracked functionally graded shaft element has been derived using fracture mechanics concepts, which is further used to develop the stiffness matrix of a cracked element. Material properties are temperature and position-dependent and graded in a radial direction following power-law gradation. A Python code has been developed to carry out the complete finite element analysis to determine the Eigenvalues and Eigenvectors of a slant-cracked rotor subjected to different thermal gradients. The analysis investigates and further reveals significant effect of the power-law index and thermal gradients on the local flexibility coefficients of slant-cracked element and whirl natural frequencies of the cracked functionally graded rotor system.