The ion transport measurements using various ion-exchange membranes (IEMs) face several challenges, including controllability, reproducibility, reliability, and accuracy. This is due to the manual filling of the solutions in two different reservoirs in a typical diffusion cell experiment with a random flow rate, which results in the diffusion through the IEM even before turning on the data acquisition system as reported so far. Here, we report the design and development of an automated experimental setup for ion transport measurements using IEMs. The experimental setup has been calibrated and validated by performing ion transport measurements using a standard nanoporous polycarbonate membrane. We hope that the present work will provide a standard tool for realizing reliable ion transport measurements using ion-exchange membranes and can be extended to study other membranes of various pore densities, shapes, and sizes.