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In this work, we study the unsteady electro-osmotic flow of fractional viscoelastic fluids in micro-parallel channels, where the velocity slip effect on the walls is also considered. The analytical solution is obtained through solving the Cauchy momentum equation, together with the linearized Poisson-Boltzmann equation and the fractional Maxwell constitutive equation. The influences of the normalized electrokinetic width K, Deborah number De, slip length L and fractional derivative 𝛼 on the velocity and volume flow rate are discussed. The results demonstrate that the dimensionless parameters L, De and K all have a promoting effect on the electro-osmotic flow and resonance behavior of fractional Maxwell fluids. In addition, compared with the classical Maxwell fluid, the microstructure of the fractional Maxwell fluid weakens the resonance behavior.