Introduction: The development of chronic kidney disease (CKD) is a common and significant complication, contributing to morbidity after liver transplantation (LT). Cytomegalovirus (CMV) infection is common in the overall population, and relevant reinfection after LT may occur. CMV-associated kidney damage has been discussed, but the clinical significance on CKD development after LT remains unclear. Methods: A total of 745 patients who underwent LT between 2006 and 2017 were included in this retrospective analysis. Clinical data, as well as laboratory parameters, were analyzed. Univariate and multivariate analysis were performed. Results: The univariate analysis revealed significantly impaired estimated glomerular filtration rates (eGFRs) in patients with histories of CMV infection (81.4 (8–137) mL/min vs. 90.0 (5–147) mL/min; p = 0.004). This effect was confirmed in the multivariate analysis. Post-LT, eGFR was impaired in patients with CMV (re)infection at 6, 12, 36, and 60 months, 10 years, and 15 years after LT. Immunosuppressive levels were comparable between groups. Overall survival was negatively affected by CMV infection (p = 0.001). Discussion: A clinically significant detrimental impact of CMV infection on renal function was observed, that could individualize clinical risk evaluation prior and after LT further. However, the pathophysiological mechanisms behind this observation are not yet understood.