This article describes the formulation and implementation of the Jk-integral for the analysis of inclined cracks located in functionally graded materials (FGMs) that are subjected to thermal stresses. The generalized definition of the Jk-integral over a vanishingly small curve at the tip of an inclined crack is converted to a domain independent form that consists of area and line integrals defined over finite domains. A numerical procedure based on the finite element method is then developed, which allows the evaluation of the components of the Jk-integral, the modes I and II stress intensity factors and the T-stresses at the crack tips. The developed procedure is validated and the domain independence is demonstrated by providing comparisons to the results obtained by means of the displacement correlation technique (DCT). Detailed parametric analyses are conducted by considering an inclined crack in an FGM layer that is subjected to steady-state thermal stresses. Numerical results show the influences of the thermal conductivity and thermal expansion coefficient variation profiles and the crack inclination angle on the mixed-mode fracture parameters.