Background: While glucocorticosteroids (GCS) are widely used in patients with kidney disease, little is known about their effect on serum creatinine, the most commonly used endogenous marker of kidney function. Methods: We assessed the effect of GCS on the relationship between estimated GFR using the Schwartz equation (eGFR) and measured GFR using a single-injection inulin clearance (Cin) in children both in a paired analysis and a cross-sectional study. Primary outcome variable was the difference between eGFR and Cin (ΔGFR) in a paired analysis involving 22 patients during and off GCS treatment (mean GFR 103.8 ml/min/1.73 m2, mean prednisone dose 34.8 mg/m2/day). In a cross-sectional analysis in 42 patients receiving GCS (mean dose of 25.7 mg/m2/day), a dose-dependent effect was explored using univariate and multivariate linear regression of various variables including GCS dosage with serum creatinine as dependent variable. Results: The paired analysis showed no significant difference in ΔGFR with or without GCS [− 23 (SD 53) vs. − 9 (SD 41) ml/min/1.73 m2, p = 0.203]. Stepwise multivariate linear regression analysis showed a significant correlation between age and Cin, while GCS dose was not related to serum creatinine. Conclusion: GCS use had no significant effect on serum creatinine as a marker for kidney function in a mixed population of renal outpatient clinic children.