Purpose To evaluate the prevalence of overweight/obesity and dyslipidemia in patients with intracranial germ cell tumor (iGCT), and to explore the risk factors of it. Methods iGCT patients visiting Peking Union Medical College Hospital between Jan 2008 to Oct 2020 were included. The prevalence of overweight/obesity and dyslipidemia was calculated. Mixed-effects models were used to evaluate the relationship between BMI z-scores, concentration of lipid profiles and potential risk factors. Results One hundred and six patients were included. The median follow-up time was 27 (IQR 5-59) months. The number of patients diagnosed with overweight/obesity and dyslipidemia were 49 (46.2%) and 86 (81.1%) during visits. Higher BMI z-scores were associated with treatment (mean difference (MD) 0.51, 95%CI 0.31-0.72), surgical biopsies (MD 0.71, 95%CI 0.16-1.25), adrenal insufficiency (MD 0.37, 95%CI 0.07-0.68), hypothyroidism (MD 0.35, 95%CI 0.06-0.63), glucocorticoid supplementation (MD 0.64, 95%CI 0.40-0.87), and thyroxine supplementation (MD 0.48, 95%CI 0.24-0.72). Hypothalamus involvement was associated with increased TC (MD 0.52, 95%CI 0.06-0.98), TG (MD 0.36, 95%CI 0.01-0.72), LDL-C (MD 0.60, 95%CI 0.20-0.98), and decreased HDL-C (MD - 0.23, 95%CI - 0.44 to - 0.02). Higher TC (MD 0.53, 95%CI 0.26-0.80) and LDL-C (MD 0.39, 95%CI 0.17-0.62) were observed in patients after treatment. Glucocorticoid supplementation was associated with increased TC (MD 0.70, 95%CI 0.38-1.03), LDL-C (MD 0.51, 95%CI 0.24-0.78), and HDL-C (MD 0.25, 95%CI 0.09-0.40), while sex hormone supplementation was associated with decreased TC (MD - 0.74, 95%CI - 1.2 to - 0.29) and TG (MD - 0.47, 95%CI - 0.86 to - 0.08). Conclusion Overweight/obesity and dyslipidemia were high prevalent in iGCT patients and should be screened during follow-ups.