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Background Postdoctoral trainees play a vital role in securing grant funding, building alliances, and mentoring graduate students under the guidance of a mentor who can help develop their intellectual independence. However, the experiences of postdoctoral trainees, particularly within health professions schools, is largely unexplored. The purpose of this study was to investigate the experiences of postdoctoral trainees and faculty advisors at a public four-year school of pharmacy and identify areas of opportunity to improve postdoctoral training. Methods Focus groups and interviews were conducted to elicit participants’ experiences, perceptions, and suggestions for improvement. Stakeholder groups included postdoctoral trainees and faculty who serve as postdoctoral advisors. Thematic coding was used to identify semantic themes, and summaries of participant perceptions were generated. Results were mapped to the identity-trajectory framework. Results Participants described various experiences related to intellectual growth, networking opportunities, and institutional support. In addition, participant agency was critical for developing career goals and navigating transitions. COVID-19 introduced unique challenges associated with transitioning to remote work and managing goals/motivation. Areas of opportunity were identified, such as improving infrastructure, enhancing mentoring, and enhancing communication. Conclusion Postdoctoral trainees play a critical role in the success of academic institutions. Scholarly endeavors that explore postdoctoral experiences, specifically those utilizing qualitative methods, can help pharmacy education better understand and meet the needs of postdoctoral trainees and faculty advisors. This study provides insight into the experiences of postdoctoral scholars and provides evidence for improving these training programs in schools of pharmacy.