In order to explore the mechanism of tribological fatigue fracture in PEEK (Poly-ether-ether-ketone) polymer mechanical element application, one-point contact type RCF (rolling contact fatigue) tests were carried out by using a PEEK shaft with an artificial defect. An alumina ball contacted a PEEK shaft specimen under maximum Hertzian stress 380 MPa. Flaking and internal fatigue crack propagation under the rolling track of the tested PEEK shaft were investigated through 2.5D layer observation method. The main fatigue crack occurred near the artificial defect on the rolling track of the PEEK shaft, and propagated into depth direction. In addition, the main fatigue crack branched due to internal shear stress. The branching crack as internal fatigue crack propagated into the ball’s rolling direction. After the linkage of the branching crack and another semicircular surface crack, the horseshoe-shaped flaking as tribological fatigue fracture occurred on the rolling track of the PEEK shaft.