Background Orthopaedic surgery has the lowest number of full-time faculty positions held by women, at 19%, with endowed chairs among the most coveted and advantageous. We examined the characteristics of endowed professors from the US top 100 orthopaedic academic centers and highest-funded musculoskeletal (MSK) researchers to determine if gender is associated with endowed professorship. Additionally, we sought to determine if gender is associated with increased NIH funding for top-performing musculoskeletal researchers. Methods Our primary study group included the top 100 orthopaedic academic centers defined by US News World Report and Doximitys rankings. Our secondary study group examined the top MSK researchers, defined as principal investigators, who received >$400,000 in annual NIH funding from 2018 to 2021. Orthopaedic departments included MSK researchers and subspecialties within orthopaedics and medicine. Publicly available sources were used to compile institutional, gender, H-index, citation number, and subspecialty data on endowed professors; statistical comparisons were calculated. Results Within the top 100 orthopaedic academic departments, 4674 faculty were identified. Seven hundred and thirty-three (15.68%) were identified as women, 3941 as men (84.32%). One hundred and ninety-four held endowed professorships; 13 were awarded to women (6.7%), and 185 (95.3%) were awarded to men, with a significant odds ratio (OR) of 2.95, favoring men. For MSK researchers, the OR increases to 11.4. Arthroplasty and sports had the highest numbers of endowments. Significant differences in H-index, publications, and graduation year were identified between men and women for top MSK researchers and orthopaedic-trained surgeons; however, these differences disappeared when considering heterogenous orthopaedic departments that included medicine subspecialties, plastic surgery, hand surgery, and neurosurgery. Additional gender differences were observed in endowment names, with awards commemorating 51.5% men, 7.2% women, and 34% families or groups. Conclusion Gender inequities at the endowment level are substantial, and there are very few women in musculoskeletal medicine to achieve endowments. Differences in H-index, publications, and graduation year between men and women MSK researchers and orthopaedic-trained surgeons, but not combined orthopaedic, PM&R, and medical subspecialty departments, suggest unique challenges in orthopaedic surgery environments and histories that may contribute to endowment disparity. Gender was not found to be associated with funding bias for top-performing musculoskeletal researchers.