Internal resistance is not a constant value. So measuring the value depends on the application.
For example, in DC there could be voltage drop under load, or voltage rise under charging. And either of these could change with time, with the state of charge, with the magnitude of the current, or with temperature (or any combination of these).
Another standard measurement is the AC impedance, which is measured by looking at an AC waveform superimposed on the cell.
So before measuring, you need to know why you are measuring, and what purpose you will use the measurement for.
For DC, you could look at two different currents and measure the two different voltages, and then compute R = ΔV/ΔI
For AC, you could pass an AC waveform through the cell, block the DC, and compute r = v/i.