Adverse effects of graft extrusion after meniscal allograft transplantation (MAT) are difficult to assess and can be determined only in the long term using a simple radiograph. Recently, subchondral bone marrow lesions (BMLs) detected on magnetic resonance imaging (MRI) scans have been used to evaluate the outcomes or prognoses of various knee surgeries. However, whether subchondral BMLs on MRI scans reflect the effects of allograft extrusion remains unclear. Subchondral BML in the lateral compartment of the knee joint on postoperative MRI scans would be associated with graft extrusion after lateral MAT. Case-control study; Level of evidence, 3. Overall, 170 patients with lateral MAT between 2008 and 2013 were classified into extrusion (≥3 mm) and nonextrusion (<3 mm) groups based on findings on MRI scans obtained 3 to 6 months postoperatively. Subchondral BMLs in the lateral compartment were evaluated on the latest MRI scans. To exclude any bone marrow signal changes other than those caused by allograft extrusion, the latest MRI scans were compared with those obtained 3 to 6 months postoperatively. Only subchondral BMLs that occurred after that time point were counted. The association between allograft extrusion and subchondral BML was assessed using chi-square analysis. Logistic regression analysis was performed to control other related factors, including age, sex, body mass index, time from previous meniscectomy, alignment, and cartilage status at the time of MAT. Clinical outcomes according to subchondral BML were evaluated using the Lysholm score. Of the 170 patients, 20 (11.8%) had subchondral BML on the latest MRI scans at a mean 53.6 ± 31.2 months postoperatively, with 14 and 6 patients in the extrusion and nonextrusion groups, respectively. Chi-square analysis showed a significant association between allograft extrusion and subchondral BMLs (P = .025). Logistic regression analysis showed that extrusion and age were significant factors associated with subchondral BML (P = .011 and .004, respectively). However, no differences were observed in the Lysholm scores in accordance with the subchondral BML (P = .248). Subchondral BMLs on postoperative MRI scans were associated with graft extrusion after lateral MAT. However, there was no difference in clinical outcomes according to subchondral BML.