Endotoxin must be controlled in the manufacturing of parenteral drug products to prevent adverse reactions in patients. Endotoxin contamination may arise in the manufacturing of active pharmaceutical ingredients when aqueous solutions are present. We describe our efforts to remove endotoxin load from a small-molecule aqueous drug substance (molecular weight 1,570 Da) that was prepared by organic synthesis and purified using preparative reverse-phase HPLC. The aqueous phosphate buffer solution used in this purification step was identified as the root cause of the endotoxin contamination. Endotoxin was removed by dead-end 10-kDa ultrafiltration at 5 °C with excellent recovery of potency and purity. Upon meeting quality release specifications, the reworked drug substance solution was used to manufacture drug product for evaluation in clinical trials.