Our objective is to assess motivation and self-regulated learning domains among undergraduate health professional students during compulsory E-learning in the COVID-19 pandemic, and explore inter-gender variabilities and the correlation between test anxiety and self-regulated learning. Institutional based descriptive study, Motivated Strategies for Learning Questionnaire (MSLQ) was administered to 291 healthy undergraduate students of health professions programs at Al Marefa University. Two months after shifting to compulsory E-learning, students were invited to return an online standardized self- administered questionnaire via Google form. Data were analyzed using SPSS version 23. Reliability analysis with an average close to or exceeds the recommended value (α = 0.7). The extrinsic motivation was higher than the intrinsic one, the use of learning strategies was modest. Female students displayed significantly higher motivation and learning strategies scores (P=0.001). Male had higher extrinsic goal orientation P= 0.001, self-efficacy P= 0.043, Help-seeking P= 0.017, while females had a higher time study environment P=0.027. Also, the youngest and oldest students were the most motivated ones (P= 0.04). A positive correlation exists between test anxiety and extrinsic goal orientation (P=0.000). Statistically significant correlations exist between test anxiety and all of the learning strategies scales. There are adequate levels of motivation with moderate use of learning strategies among health professional students during sudden shifting to compulsory E-learning in the COVID-19 pandemic. Females’ students were more self-regulated learners than males. Further investigation of the use of the Motivated Strategies for Learning Questionnaire and its association with academic achievement is recommended to assess the online teaching experience.