The uranyl-selenate system is studied in aqueous acid solutions (pH 2.5) at different values of the ionic strength (from 0.02 to 0.1 mol L−1) in the temperature range from 15 °C to 55 °C by affinity capillary electrophoresis. Hydrodynamic transfer of the sample through the non-thermostated inlet into the thermostated region of capillary is used to avoid the influence of non efficiently thermostated short inlet. The formation of two complex species UO2SeO4 and UO2(SeO4)22− is observed. Thermodynamic parameters (the molar Gibbs energy of reaction (ΔrGm), the molar enthalpy of reaction (ΔrHm) and the molar entropy of reaction (ΔrSm)) are calculated and extrapolated to zero ionic strength with aid of specific ion interaction theory. Results show that complex species of uranyl with selenate become stronger as the temperature is increased. The complexation is endothermic and entropy-driven, showing typical characteristics of inner-sphere complexation between hard acceptor and hard donor.