We extend the Zee model by introducing a vector-like lepton doublet and a flavor dependent global $U(1)$ symmetry. Flavor changing neutral currents in the quark sector can be naturally forbidden at tree level due to the $U(1)$ symmetry, while sufficient amount of lepton flavor violation is provided to explain current neutrino oscillation data. In our model, additional sources of CP-violation appear in the lepton sector, but their contribution to electric dipole moments is much smaller than current experimental bounds due to the Yukawa structure constrained by the $U(1)$ symmetry. We find that there is a parameter region where the strongly first order electroweak phase transition can be realized, which is necessary for the successful scenario of the electroweak baryogenesis in addition to new CP-violating phases. In the benchmark points satisfying neutrino data, lepton flavor violation data and the strongly first order phase transition, we show that an additional CP-even Higgs boson $H$ mainly decays into a lighter CP-odd Higgs boson $A$, i.e., $H to AZ$ or $H to AA$ with a characteristic pattern of lepton flavor violating decays of $A$.