Background/Objectives: The optimal graft, particularly in combined anterior cruciate ligament (ACL) and medial collateral ligament (MCL) injuries, remains controversial. We evaluated the influence of graft choice between bone-patellar tendon-bone (BPTB) and hamstring autografts on clinical outcomes in combined ACL and MCL injuries. Methods: This retrospective analysis included patients with concurrent ACL and MCL injuries who underwent single-bundle ACL reconstruction with BPTB (group B) or hamstring (group H) grafts, between 2010 and 2019, with a ≥2-year follow-up. Patients were classified based on the MCL injury grade (I, II, or III). Clinical outcomes were assessed through knee stability evaluations using valgus stress radiographs and the KT-2000 arthrometer, patient-reported outcomes using the International Knee Documentation Committee (IKDC) subjective score and Lysholm score, and radiologic outcomes using the IKDC radiographic grade. Results: The study included 169 patients (group B, 92; group H, 77). No significant between-group differences in knee stability or functional outcomes were found after follow-up. Within the same MCL injury grade, particularly in high-grade MCL injuries, BPTB grafts resulted in significantly better medial stability (side-to-side difference in medial joint opening on valgus stress radiographs: grade II, p = 0.006; grade III, p = 0.039) and functional outcomes (IKDC subjective score: grade II, p = 0.045; grade III, p = 0.038) than hamstring grafts. In the hamstring group, higher-grade MCL injuries were associated with worse outcomes (Lysholm knee score, p = 0.009; IKDC subjective score, p = 0.015). Conclusions: Graft choice in ACL reconstruction with concomitant MCL injuries may affect clinical outcomes, particularly in high-grade MCL injuries. Although both graft types performed similarly overall, BPTB grafts provided superior medial stability and functional results in higher-grade MCL injuries. However, caution is needed when interpreting these results due to limitations such as the small sample size and the lack of randomization in graft selection.