Matrix stones are a rare form of kidney stones, which are composed of mucoproteinaceous material. They are often difficult to diagnose as they are characteristically radiolucent on CT urinary tract. This difficulty is compounded in transplanted kidneys as obstructing stones commonly present without pain and can cause acute kidney injury. Here, we present a case of a 61-year-old female with a live-donor kidney transplant, who was found to develop deranged renal function on routine follow-up investigations. Therefore, a CT urogram was performed and it showed filling defects in the renal pelvis and upper ureter of the transplanted kidney. Therefore, diagnostic ureterorenoscopy was performed and three stones of about 7-8 mm each were found in the renal pelvis, they were treated by Holmium:Yttrium aluminium garnet (YAG) laser fragmentation. This case report describes the challenges in the management of this rare stone in a transplanted kidney.