Functionally graded materials provide versatility in adjusting the volume fractions of constituent materials to meet specific design requirements. However, this customization often introduces mode-mixity at the crack tip, posing challenges in predicting fracture under cyclic loading with discrete approaches and computationally expensive with conventional phase-field fracture models. To address these issues, this paper introduces an adaptive phase-field fracture formulation with cycle jump scheme to elegantly predict fatigue crack nucleation and growth in functionally graded materials. Within this framework, the effective properties at a point are estimated using the Mori–Tanaka homogenization scheme, while the crack growth due to cyclic load is captured by incorporating an additional fatigue degradation parameter. Moreover, the computational efficiency of the proposed framework is improved through an adaptive mesh refinement and explicit cycle jump scheme. The adaptive refinement scheme utilizes an error indicator derived from both the displacement solution and phase-field variable. The adaptive refinement scheme is integrated with efficient quadtree decomposition, which generates a hierarchical mesh structure. Hanging nodes resulting from the quadtree decomposition are efficiently handled using a polygonal finite element method. The proposed framework is validated against experimental and numerical results reported in the literature. Furthermore, we investigate the fatigue crack growth resistance across a broad range of material gradation directions, gaining valuable insights and identifying functionally graded materials with high fatigue resistance.