Glycogen storage disease type Ia (GSDIa) is a rare, inherited glucose-6-phosphatase-α (G6Pase-α) deficiency-induced carbohydrate metabolism disorder. Although hyperlipidaemia is a hallmark of GSDI, the extent of lipid metabolism disruption remains incompletely understood. Lipidomic analysis was performed to characterise the serum lipidome in patients with GSDIa, by including age- and sex-matched healthy controls and age-matched hypercholesterolemic controls. Metabolic control and dietary information biochemical markers were obtained from patients with GSDIa. Patients with GSDIa showed higher total serum lysophosphatidylcholine (Fold Change, FC 2.2, p < 0.0001), acyl-acyl-phosphatidylcholine (FC 2.1, p < 0.0001), and ceramide (FC 2.4, p < 0.0001) levels and bile acid (FC 0.7, p < 0.001), acylcarnitines (FC 0.7, p < 0.001), and cholesterol esters (FC 1.0, p < 0.001) than those of healthy controls, and higher di- (FC 1.1, p < 0.0001; FC 0.9, p < 0.01) and triacylglycerol (FC 6.3, p < 0.0001; FC 3.9, p < 0.01) levels than those of healthy controls and hypercholesterolemic subjects. Both total cholesterol (TC) and TG values correlated with Cer(d16:1/22:0), Cer(d18:1/20:0), Cer(d18:1/20:0(OH)), Cer(d18:1/22:0), Cer(d18:1/23:0), Cer(d18:1/24:1), Cer(d18:2/22:0), Cer(d18:2/24:1). TC also correlated with Cer(d18:1/24:0), Cer(d18:2/20:0), HexCer(d16:1/22:0), HexCer(d18:1/18:0), and Hex2Cer(d18:1/20:0). TGlevels correlated with Cer(d18:0/24:1). Alanine transaminase values correlated with Cer(d18:0/22:0), insulin with Cer(d18:1/22:1) and Cer(d18:1/24:1), and HDL with hexosylceramide (HexCer)(d18:2/23:0). These results expand on the currently known involvement of lipid metabolism in GSDIa. Circulating Cer may allow for refined dietary assessment compared with traditional biomarkers. Because specific lipid species are relatively easy to assess, they represent potential novel biomarkers of GSDIa.