Background: Increasingly, national programs and leaders are looking at interdisciplinary collaborations as essential to future research. Twelve years ago, the National Institutes of Health (NIH) Office of Research on Women's Health (ORWH) developed and implemented the Building Interdisciplinary Research Careers in Women's Health (BIRCWH) K12 program to focus on interdisciplinary mentored career development for junior faculty in women's health research. Methods: We applied a mixed-methods approach using an electronic survey and in-person presentations and discussions to understand best practices and lessons learned for interdisciplinary mentoring across BIRCWH K12 program leaders. Results and Conclusions: We received responses from all 29 active BIRCWH programs. Factors associated with success included ensuring sufficient protected time for regular (weekly or biweekly) mentoring; mentors promoting the research independence of the Scholar; a team mentoring approach, including career as well as content mentors; and explicit and clear expectations outlined between the Scholar and mentor. The majority of programs conduct formal evaluations of mentorship, and 79% of programs offer training in mentorship for either Scholars, mentors, or both. This article presents program leaders' best practices, challenges, and lessons learned from mentoring junior faculty who are conducting women's health research, whether basic, clinical, behavioral, translational, or health services research, using an interdisciplinary mentoring approach.