IntroductionMentorship is an essential component of research capacity building for young researchers in the health sciences. The mentorship environment in resource-limited settings is gradually improving. This article describes mentees’ experiences in a mentorship program for junior academicians amid the COVID-19 pandemic in Tanzania.MethodsThis is a survey study that examined the experiences of mentees who participated in a mentorship program developed as part of the Transforming Health Education in Tanzania (THET) project. The THET project was funded by the US National Institutes of Health (NIH) under a consortium of three partnering academic institutions in Tanzania and two collaborating US-based institutions. Senior faculty members of respective academic institutions were designated as mentors of junior faculty. Quarterly reports submitted by mentees for the first four years of the mentorship program from 2018 to 2022 were used as data sources.ResultsThe mentorship program included a total of 12 mentees equally selected from each of the three health training institutions in Tanzania. The majority (7/12) of the mentees in the program were males. All mentees had a master’s degree, and the majorities (8/12) were members of Schools/Faculties of Medicine. Most mentors (9/10) were from Tanzania’s three partnering health training institutions. All mentors had an academic rank of senior lecturer or professor. Despite the onset of the COVID-19 pandemic, the regular weekly meetings between mentors and mentees were not affected. By the fourth year of the mentorship program, more than three-quarters of mentees had published research related to the mentorship program in a peer-reviewed journal, over half had enrolled in Ph.D. studies, and half had applied for and won competitive grant awards. Almost all mentees reported being satisfied with the mentorship program and their achievements.ConclusionThe mentorship program enhanced the skills and experiences of the mentees as evidenced by the quality of their research outputs and their dissemination of research findings. The mentorship program encouraged mentees to further their education and enhanced other skills such as grant writing. These results support the initiation of similar mentorship programs in other institutions to expand their capacity in biomedical, social, and clinical research, especially in resource-limited settings, such as Sub-Saharan Africa.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12909-023-04369-z.