The ion-partitioning effects on solute transport phenomena of time-periodic electro-osmotic flow in fractional Jeffrey fluid are investigated through a polyelectrolyte layer (PEL)-coated conical nanopore within a reactive wall whose ends are connected with two large reservoirs. By considering the ion-partitioning effects, analytical solutions for the induced potential and the axial velocity are presented, respectively, from the modified Poisson–Boltzmann equation and the Cauchy momentum equation with the proper constitutive equation of the fractional Jeffrey fluid model in the exterior and interior of the PEL. The analytic solution of the convection–diffusion for solute transport is established in the entire domain. The influence of the oscillating Reynolds number Rew, permittivity ratio εr between two mediums, relaxation time λ1ω, retardation time λ2ω, phase partitioning coefficient σp, PEL fixed charge density qfix, Debye–Hückel parameter κa, and softness parameter λs are investigated in this study. Asymptotic solution for the axial velocity was also presented for low-oscillating Reynolds numbers and validated. The maximum axial velocity occurs when the permittivity between the PEL and electrolyte is the same for all models. The volumetric flow rate decreases with the increase in the PEL thickness, positive PEL charge density, and softness parameter in our study. The volume flow rate of the Newtonian fluid increased 24.07% for Maxwell fluid (λ1ω=5, α = 1) and 11.56% for Jeffrey fluid (λ1ω=5, λ1ω=1, α = 1, and β=0.5), when κa=25, Rew = 10, qfix = 5, d = 0.2, εr=0.6, and λs=1.0. The mass transport rate increases with relaxation time, tidal displacement, and permittivity ratio between these layers.