Background E-Learning solutions are increasingly being advocated to augment existing traditional teaching and learning efforts in health training institutions. Unfortunately, these emerging technologies rarely focus on health sciences education within the context of public universities, hence the need for this study. This project evaluated experiences of healthcare trainees with a pilot e-Learning project (SMART e-Learning project) initiated in one of Ghana’s public universities in 2017. The study used a mixed methods cross-sectional approach among 363 healthcare trainees. Data collection was between 17th October, 2019 to 3rd December, 2019. Data was analysed descriptively and test for variable differences done using Pearson Chi-square and Fisher’s Exact for categorical variables. Wilcoxon Mann-Whitney test was used to test for differences in the Likert scale items. Additionally, rotated varimax factor analysis was performed for the health trainees’ rated satisfaction factors. Results Out of 446 respondents who consented to participate in the study, 363 responses were complete and valid, representing a response rate of 81 %. Most frequently used e-learning facilities by healthcare trainees were: writing interim assessments (IAs) (82 %) while the least used function was live chating with faculty (5 %). Challenges associated with the e-learning pilot project were: limited workspace in the pilot computer laboratory (33 %), slow internet/intranet speed (29 %) and limited capacity of teaching and ICT staff to support users (28 %). Conclusions There is the need to engage relevant stakeholders at the University, ministries of health and education through policy dialogues to develop statutory e-Learning guidelines for health educational institutions of higher learning to complement existing traditional teaching and learning approaches.