Elevated levels of thyroid-stimulating-hormone (TSH) are associated with reduced glomerular filtration rate (GFR) and increased risk of developing chronic kidney disease even in euthyroid patients. Thyroid hormone replacement therapy has been shown to delay progression to end-stage renal disease in sub-clinically hypothyroid patients with renal insufficiency. However, such associations after kidney transplantation were never investigated. In this study the association of thyroid hormones and estimated GFR (eGFR) in euthyroid patients after kidney transplantation was analyzed. In total 398 kidney transplant recipients were assessed retrospectively and association between thyroid and kidney function parameters at and between defined time points, 12 and 24 months after transplantation, was studied. A significant inverse association was shown for TSH changes and eGFR over time between months 12 and 24 post transplantation. For each increase of TSH by 1 µIU/mL, eGFR decreased by 1.34 mL/min [95% CI, -2.51 to -0.16; p = 0.03], corresponding to 2.2% eGFR decline, within 12 months. At selected time points 12 and 24 months post transplantation, however, TSH was not associated with eGFR. In conclusion, an increase in TSH between 12 and 24 months after kidney transplantation leads to a significant decrease in eGFR, which strengthens the concept of a kidney-thyroid-axis.