Clerkship evaluations play a critical role in assessing medical student performance and informing residency selection, yet little is known about how evaluator characteristics may influence grading patterns in clinical education. Prior studies have identified gender-related differences in narrative feedback and numerical evaluations of medical trainees, although findings remain inconsistent across specialties and institutions. This study examined whether preceptor gender and student gender were associated with differences in numerical clerkship evaluation scores among third-year medical students. A retrospective analysis was conducted using 6,855 clerkship evaluations from students in the graduating classes of 2022-2024 at a U.S. osteopathic medical school. Evaluations were completed by 2,425 preceptors across six required clerkships: Family Medicine, Internal Medicine, Obstetrics and Gynecology, Pediatrics, Psychiatry, and Surgery. The cohort included 3,978 male students and 2,877 female students. Associations between preceptor gender, student gender, and evaluation scores were analyzed using generalized linear mixed models while accounting for academic year and clerkship rotation. Preceptor gender was significantly associated with evaluation scores, with female preceptors assigning modestly lower Total Average and Clinical Competence scores than male preceptors (p < 0.0001). Student gender demonstrated smaller effects, with female students receiving slightly higher Total Average scores (p = 0.0260) and Professionalism scores (p = 0.0026). No significant interaction between preceptor and student gender was observed. Clerkship rotation was strongly associated with evaluation scores, with higher adjusted scores in Family Medicine and Pediatrics and lower scores in Surgery and Internal Medicine. As this study was conducted at a single institution, generalizability may be limited. These findings suggest that evaluator characteristics and specialty-specific grading cultures may influence clinical assessment and highlight the potential value of increased standardization and preceptor training in clerkship grading.