The COVID-19 pandemic is a major threat to global education. Incidental emotions of fear and anxiety during pandemic have unconsciously influenced preference and outcome about their future career. This study aimed to assess the effect of the COVID-19 pandemic towards career preference change in medical students. A total of 1,027 responses from all over the medical students in Indonesia were collected from an online questionnaire which was broadcasted through social media from 14th July 2020-21st July 2020. This study was using Fear of COVID-19 Scale (FCV-19S) and Depression Anxiety Stress-Scale-21 (DASS-21) to assess fear of COVID-19, stress, anxiety, and depression. Out of 1,027 respondents, 44.6% had stressed, 47.8% had anxiety, and 18.5% had depression with an average FCV-19S score was 17.1. The result showed that the fear and anxiety of COVID-19 during the pandemic had associated significantly with the career decisions in medical students (p=<0.05). Indonesian policymakers had to keep in mind that the fear of the COVID-19 pandemic in medical students is due to the high mortality COVID-19 cases of health workers in Indonesia. Health workers need adequate working conditions and specific protection, this requires prompt attention from stakeholders.