A new method has been developed to improve the determination of thiocyanate using isotachophoresis. This method uses complexation with copper(II) as a mechanism for improving the separation of thiocyanate from chlorate and perchlorate. By using a pH of 3.25 the method can also be used to analyse nitrite. Separations were carried out using a miniaturised poly(methyl methacrylate) (PMMA) separation device. Linearity was observed from 1.25 to 75 mg dm−3 with a correlation coefficient of 0.998 for both thiocyanate and nitrite. Limits of detection for these two species were calculated to be 0.8 mg dm−3 and 0.9 mg dm−3 respectively. The method was successfully applied to the analysis of these anions in a range of samples including explosive residues.