© Copyright © 2021 Bilgi, Aytaş, Karatoprak, Kazancıoǧlu and Özçelik.Introduction: The coronavirus disease 2019 (Covid-19) pandemic has influenced the whole world, where after the first case was diagnosed in Turkey, educational activities were suspended and partial curfews were implemented. This study was conducted to assess the concerns faced by the medical students about their professional life due to the disrupted educational activities and related psychological effects. Methods: This is a cross-sectional survey study, conducted with self-administered questionnaires on Bezmialem Vakif University medical students, during the pandemic. The questionnaire consists of queries about demographics, environmental factors, Generalized Anxiety Disorder-7 (GAD-7), and Patient Health Questionnaire-9 (PHQ-9) scales. Results: A total of 178 students participated in the study, with a female-to-male ratio of 5:2. Of the total respondents, 19.7% were experiencing severe anxiety, 17.4% moderate anxiety, and 37.1% mild anxiety, according to the GAD-7; and 13.5% of the respondents were experiencing severe depression, 21.9% moderate–severe depression, and 23% mild depression according to the PHQ-9. There was no statistically significant difference between the grades in terms of GAD-7 or PHQ-9 scores. Male participants were more likely to have suicidal thoughts (p = 0.013). According to our study, the factors with the highest influence on students were as follows: “Major changes in personal life,” “Disruption in educational activities,” and “Covid-19 related anxiety of loss of relatives and contamination or infection.” On average, women voted higher points for “Covid-19 related anxiety of loss of relatives and contamination.” Conclusions: We found that a significant portion of students regardless of their year in medical school were profoundly affected by the pandemic process as is shown by their anxiety and depression scores. The disruption in educational activities is one of the main factors of these effects, and we believe that these should not be ignored, as they could in the future lead to a series of problems for medical education and students alike.