In this study, a class of delayed fractional-order predation models with disease and cannibalism in the prey was studied. In addition, we considered the prey stage structure and the refuge effect. A Holling type-II functional response function was used to describe predator–prey interactions. First, the existence and uniform boundedness of the solutions of the systems without delay were proven. The local stability of the equilibrium point was also analyzed. Second, we used the digestion delay of predators as a bifurcation parameter to determine the conditions under which Hopf bifurcation occurs. Finally, a numerical simulation was performed to validate the obtained results. Numerical simulations have shown that cannibalism contributes to the elimination of disease in diseased prey populations. In addition, the size of the bifurcation point τ0 decreased with an increase in the fractional order, and this had a significant effect on the stability of the system.