Background Classical galactosaemia (OMIM #230400) is a rare disorder of carbohydrate metabolism caused by deficiency of the galactose-1-phosphate uridyltransferase enzyme. The pathophysiology of the long-term complications, mainly cognitive, neurological and female fertility problems, remains poorly understood. Current clinical methods of biochemical monitoring lack precision and individualization with an identified need for improved biomarkers for this condition. Methods We report the development and detailed validation of an automated ultraperformance liquid chromatography N-glycan analytical method of high peak resolution applied to galactose incorporation into human serum IgG. Samples are prepared on 96-well plates and the workflow features rapid glycoprotein denaturation, enzymatic glycan release, glycan purification on solid-supported hydrazide, fluorescent labelling and post-labelling clean-up with solid-phase extraction. Results This method is shown to be accurate and precise with repeatability (cumulative coefficients of variation) of 2.0 and 8.5%, respectively, for G0/G1 and G0/G2 ratios. Both serum and processed N-glycan samples were found to be stable at room temperature and in freeze–thaw experiments. Conclusions This high-throughput method of IgG galactose incorporation is robust, affordable and simple. This method is validated with the potential to apply as a biomarker for treatment outcomes for galactosaemia.