This study developed a methodology to analyze trace rare earth elements (REEs) in geological materials by capillary electrophoresis (CE). Changed from dilute HNO3 into a water medium by heating, REE ions are detectable at approximately 2 ng mL(-1). In the presence of coexisting elements from geological samples, REE separations were carried out. After sample fusion with Na2O2 and interference separation with ammonium pyrrolidinedithiocarbamate chelate, REE analytes were coprecipitated with Mg(OH)2 at pH 8.5, and then prepared into a water medium for CE determination. Using the standard addition method, this protocol was validated by analyses with better than 5% precision. This method was applied to geological materials; the REE results are in consistence with their certified values. With electrokinetic injection, internal standard (IS) selected among lanthanides is a prerequisite of high-quality REE data. An approach was proposed to derive the IS content for further correcting its contribution from unknown samples.