Background: The Covid-19 pandemic has become a worldwide disaster. The Covid-19 pandemic has impacted all sectors of life, including medical education. Medical student competence was decreased during online learning during the Covid-19 pandemic. This study aims to explore the perceptions of teachers and students toward medical science competence when viewed from the aspect of knowledge, skills, and effectiveness. Methods. The research approach used qualitative methods with a phenomenological approach and the data collected data with interviews and focus group discussions (FGD). The population was all undergraduate medical education students who were still active. Participants were determined by the purposive sampling method. Analysis of qualitative data by making transcripts, coding, and thematic analysis. Results. The perception of teachers and students towards the competence of clinical and affective skills of online learning students was lower than offline learning. Knowledge competence in online learning was almost the same as in offline learning. Conclusions. The competence of clinical and affective skills was not achieved by students but the knowledge competence was achieved in online learning during the Covid-19 pandemic.