We study colored Higgsino-mediated proton decay (dimension-five proton decay) in a model based on the flipped SU(5) GUT. In the model, the GUT-breaking 10, $$ \overline{\mathbf{10}} $$
10
¯
fields have a GUT-scale mass term and gain VEVs through higher-dimensional operators, which induces an effective mass term between the color triplets in the 5, $$ \overline{\mathbf{5}} $$
5
¯
Higgs fields that is not much smaller than the GUT scale. This model structure gives rise to observable dimension-five proton decay, and at the same time achieves moderate suppression on dimension-five proton decay that softens the tension with the current bound on Γ(p → K+$$ \overline{\nu} $$
ν
¯
). We investigate the flavor dependence of the Wilson coefficients of the operators relevant to dimension-five proton decay, by relating them with diagonalized Yukawa couplings and CKM matrix components in MSSM, utilizing the fact that the GUT Yukawa couplings are in one-to-one correspondence with the MSSM Yukawa couplings in flipped models. Then we numerically evaluate the Wilson coefficients, and predict the distributions of the ratios of the partial widths of various proton decay modes.