The interface optical (IO) phonon-assisted electron scattering rates in wurtzite GaN-based asymmetrical step quantum wells (QWs) are theoretically investigated by adopting the usual Fermi golden rule. Based on the dielectric continuum model and Loudon’s uniaxial crystal model, the analytical IO phonon states and their dispersive equation as well as the Fröhlich electron–phonon interaction Hamiltonian are derived. Taking into consideration the effects of strong built-in electric field (BEF) and the band nonparabolicity, the exact electronic eigen-states in the step QW are obtained with the aid of the two Airy functions. Numerical calculations on a wurtzite AlN/GaN/AlxGa1−xN/AlN step QW are performed. It is found that there are four branches of IO phonon modes in the asymmetric nitride step QWs, which is obviously different from the situation of symmetrical GaN/AlN single and coupling QWs. This is mainly ascribed to the asymmetry of the step QW structures studied here. The calculated results show that the intrasubband and intersubband scattering rates in wurtzite step QWs are one order of magnitude larger than those in GaAs-based step QWs, which is attributed to the larger electron–phonon coupling constants of GaN-based materials. The intrasubband scattering rates in wurtzite step QWs depend on the structural parameters in a similar manner as in cubic GaAs-based step QWs, but the intersubband scattering rates here show obviously different dependent behavior on the structural parameters. This is ascribed to the effects of the strong BEF and the band nonparabolicity. Moreover, the high-frequency IO modes play more important role to the total scattering rates than the low-frequency ones. And the contributions of the low-frequency IO modes could be neglected when analyzing the electron–phonon scattering processes in wurtzite step QWs.