This study was to investigate the deposition and elimination of glucosinolate metabolites including 5-vinyl-1,3-oxazolidine-2-thione (5-VOT) and thiocyanate ion (SCN) derived from rapeseed meal (RSM) in hen eggs. During 12 weeks accumulation phase, the serum triiodothyronine, thyronine, blood urea nitrogen, kidney index, and thyroid index linearly increased with the RSM at week 12 (P < 0.05). The thyroid histopathology revealed a sign of hyperplastic goiter in hens fed with 17.64-29.40% RSM. The 5-VOT content of eggs (Y, ng/g) was correlated with 5-VOT intake (X, μg/d·bird) and 5-VOT feeding time (X, week): Y = 54.94X + 0.51X - 430.34 (P < 0.01, R = 0.80). The SCN content of eggs (Y, mg/kg) was correlated with RSM intake (X, μg/d·bird) and RSM feeding time (X, week): Y = 0.095X + 0.302X - 0.4211 (P < 0.01, R = 0.70). After a 4-week withdrawal of RSM, the 5-VOT and SCN did not show in eggs. Taken together, 5.88% RSM with dietary supplements of 23.55 mg/kg 5-VOT and 10.76 mg/kg SCN had no effects on hens with regard to serum parameters, organ index, and thyroid histopathology, and more than 4 weeks withdrawal should be considered for human and hen health.