Knee subchondroplasty (SCP) is one of the most novel minimally invasive methods for treating bone marrow lesions. The literature suggests that it is safe, with few complications and good outcomes. However, no studies have documented its usage for managing large subchondral bone cysts. This article outlines a case report and details the pearls and pitfalls of SCP in treating large subchondral bone cysts. Our patient underwent arthroscopic debridement with medial femoral condyle SCP. Mild posterior extravasation of synthetic bone substitute was observed on Postoperative Day 1, which was immediately rectified on revision arthroscopy. Gradual escalation of weight bearing and good pain relief were subsequently achieved, and the patient has remained complication-free after two years. No further extravasation were observed on repeat radiography. SCP is a feasible temporising measure that may help to delay the need for bone allograft or immediate knee arthroplasty in younger patients while retaining function and delaying loss of productivity.