The ideal circumstances for whether and when to start RRT remain unclear. The outcome predictive ability of acute kidney injury (AKI) biomarkers measuring at dialysis initializing need more validation. This prospective, multi-center observational cohort study enrolled 257 patients with AKI undergoing renal replacement therapy (RRT) shortly after admission. At the start of RRT, blood and urine samples were collected for relevant biomarker measurement. RRT dependence and all-cause mortality were recorded up to 90 days after discharge. Areas under the receiver operator characteristic (AUROC) curves and a multivariate generalized additive model were applied to predict outcomes. One hundred and thirty-five (52.5%) patients died within 90 days of hospital discharge. Plasma c-terminal FGF-23 (cFGF-23) had the best discriminative ability (AUROC, 0.687) as compared with intact FGF-23 (iFGF-23) (AUROC, 0.504), creatinine-adjusted urine neutrophil gelatinase-associated lipocalin (AUROC, 0.599), and adjusted urine cFGF-23 (AUROC, 0.653) regardless whether patients were alive or not on day 90. Plasma cFGF-23 levels above 2050 RU/mL were independently associated with higher 90-day mortality (HR 1.76, p = 0.020). Higher cFGF-23 levels predicted less weaning from dialysis in survivors (HR, 0.62, p = 0.032), taking mortality as a competing risk. Adding cFGF-23 measurement to the AKI risk predicting score significantly improved risk stratification and 90-day mortality prediction (total net reclassification improvement = 0.148; p = 0.002). In patients with AKI who required RRT, increased plasma cFGF-23 levels correlated with higher 90-day overall mortality after discharge and predicted worse kidney recovery in survivors. When coupled to the AKI risk predicting score, cFGF-23 significantly improved mortality risk prediction. This observation adds evidence that cFGF-23 could be used as an optimal timing biomarker to initiate RRT.