The aim of this study was to develop a fast method of screening for orotic acid in untreated urine by capillary electrophoresis with using a combination of two capillaries with different internal diameters, 50 μm and 100 μm. Under the optimized conditions, 100 mM sodium phosphate buffer pH 2.2, voltage of 5 kV, hydrodynamic injection at 50 mbar for 5 s, and detection at 214 nm, the migration time of orotic acid was only 2.1 min. The validation of the method resulted in orotic acid recoveries of 96.5 ± 0.8%. We achieved good precision with RSD of migration times at less than 0.8% and peak areas lower than 3.1% intraday precision. We obtained a very good linearity in the validated range 1–100 μmol L−1, R2 0.9993, and a limit of detection of 2.4 μmol L−1. Finally, we proved that the method is robust, including the connection of capillaries, using the Youden test.