The COVID-19 pandemic has disrupted the teaching and learning process at various universities, especially for health science students. Electronic learning (E-Learning) is applied as a core learning method to carry out learning during the pandemic. This study aimed at investigating health science students’ perception about the quality of their online learning during the pandemic. A mixed method research design was implemented in this current study. The modified version of Online Learning Environment Survey (OLES) was used as the main instrument to collect data from 390 health science students at 'Aisyiyah University in Yogyakarta consisting of seven study programs such as nursing, anesthesiology, midwifery, physiotherapy, nutrition, medical lab technology and radiology. Contrary assumption from the previous research, this study found that there were only slight differences between students from the seven study programs with regard to their perception of online learning. Majority of students agreed that during pandemic they have studied real cases and considered to be relevant to issues that occur outside the classroom. However, in health science education system where many courses are practical oriented, students confirmed that shifting completely to online mode may not be possible to enhance their skill to become a professional medical in the future. Therefore, it is prominent to design an effective curriculum for health science education system for the new normal.