Amphiphilic diblock copolymers consisting of a hydrophobic core containing a polymerized ionic liquid and an outer shell composed of poly(N-isoprolylacrylamide) were investigated by capillary electrophoresis and asymmetrical flow-field flow fractionation. The polymerized ionic liquid comprised poly(2-(1-butylimidazolium-3-yl)ethyl methacrylate tetrafluoroborate) with a constant block length (n = 24), while the length of the poly(N-isoprolylacrylamide) block varied (n = 14; 26; 59; 88). Possible adsorption of the block copolymer on the fused silica capillary, due to alterations in the polymeric conformation upon a change in the temperature (25 and 45 °C), was initially studied. For comparison, the effect of temperature on the copolymer conformation/hydrodynamic size was determined with the aid of asymmetrical flow-field flow fractionation and light scattering. To get more information about the hydrophilic/hydrophobic properties of the synthesized block copolymers, they were used as a pseudostationary phase in electrokinetic chromatography for the separation of some model compounds, that is, benzoates and steroids. Of particular interest was to find out whether a change in the length or concentration of the poly(N-isoprolylacrylamide) block would affect the separation of the model compounds. Overall, our results show that capillary electrophoresis and asymmetrical flow-field flow fractionation are suitable methods for characterizing conformational changes of such diblock copolymers.