Advanced glycation end products (AGEs), produced by the Maillard reaction between carbohydrates and proteins, may be involved in diabetes and its complications. Accurate quantification of AGEs in vivo can demonstrate the relation between AGEs and pathological conditions, but it is not widely used in clinical practice because of the multiple pretreatment steps before analyses. We developed a fully automated solid-phase extraction system (FSPES) to simplify rate-limiting pretreatment using a cation exchange column. We applied this device to evaluate AGEs in nephropathy. Among the standard samples, we used arginine, lysine, N‍^ε-(carboxymethyl)lysine (CML), N‍^ω-(carboxymethyl)arginine (CMA), N‍^ε-(carboxyethyl)lysine (CEL), and N‍^δ-(5-hydro-5-methyl-4-imidazolone-2-yl)-ornithine (MG-H1) for FSPES. We analyzed the coefficient of variation (CV) by mass spectrometry. FSPES performed column operations rapidly at a pressure three times higher compared with the conventional method. FSPES stably performed pretreatment. CV results for CML, CMA, CEL, and MG-H1 measurements in bovine and human serum were the same as those in the conventional pretreatment. Among the AGE structures we measured, CML and CEL increased with the decline in kidney function. The CML and CEL levels of patients with nephropathy were significantly higher than those in normal subjects. Thus, FSPES is useful for clarifying the relation between AGEs and various pathological conditions.