Chronic kidney disease (CKD) is common after heart transplantation (HT). There are scarce studies looking at longitudinal changes in estimated glomerular filtration rate (eGFR) after repeat HT (RT) and risk factors for the presence of CKD3 post-RT. First-time HT recipients (FT) were matched with RT, based on age at transplant, sex, race, and transplant era. eGFR was derived from CKiD-U25 formula using creatinine. Changes in eGFR were measured within and between patients using a mixed effects model. Logistic regression and survival analysis were performed to identify significant risk factors for CKD3 presence post-RT. The unmatched cohort included 393 HT recipients and 47 RT. 29 patients in both groups with at least 2 years of follow-up data underwent matching. Over 6 years, the mean eGFR for FT and RT did not significantly change overtime. For those with CKD3 or higher prior to RT, 73% improved to CKD2 or lower at 2 years post-RT. Risk factors for CKD3 post-RT included female sex (OR 17.5 [1.7-181.9], p = 0.017) and greater than two acute kidney injuries (AKI) between FT and RT (OR 1.77 [1.06-2.95], p = 0.03). Approximately 50% of females and those with greater than two AKIs maintained or developed CKD3 at 7.5 and 3 years, respectively. This study provides data on longitudinal changes in eGFR over 6 years and finds that female sex and repeat HT recipients with greater 2 AKIs between transplants are at greatest risk for CKD3 presence post-RT.