Background <p>Previously, it was reported that preoperative medial tibial bone marrow lesions (BMLs) were not associated with worse postoperative outcomes after medial unicompartmental knee arthroplasty (UKA). However, the effect of BMLs in the tibial intercondylar eminence (ICE), which may represent heterogeneous lesions with different underlying mechanisms, on postoperative clinical outcomes has not yet been reported. The aim of this pilot study was to investigate the effect of BMLs in the tibial ICE on postoperative clinical outcomes after UKA.</p> Methods <p>Eighty-three patients who underwent UKA with preoperative magnetic resonance imaging (MRI) were enrolled. Patients were divided into two groups according to the presence or absence of BMLs in the tibial ICE. Preoperative and postoperative clinical outcomes at two-year follow-up were evaluated and compared between the two groups using the 2011 Knee Society Knee Scoring System (2011 KSS) with unpaired t-test. The incidence of complications was compared between the groups using Fisher’s exact test.</p> Results <p>There were 39 and 44 patients in the BML and no-BML groups, respectively. Significant improvements in all parameters according to the 2011 KSS after UKA were observed in both groups. There was no significant difference in the degree of improvement in all parameters of the 2011 KSS between the two groups. Radiolucent lines (RLs) around the tibial component were observed in three patients in each group. No patient had a postoperative periprosthetic fracture or infection. There was no significant difference in the incidence of RLs, periprosthetic fracture and infection.</p> Conclusions <p>Preoperative BMLs in the tibial ICE were not associated with poor short-term clinical outcomes in this cohort.</p>