Purpose: The development of students’ clinical reasoning skills should be a consideration in the design of instruction and evaluation in medical education. In response to the coronavirus disease 2019 (COVID-19) pandemic, several changes in the medical curriculum have been implemented in promoting clinical reasoning. This study aims to explore medical students’ perceptions and experiences with the clinical reasoning curriculum during the COVID-19 pandemic and determine their skills development. Methods: The study used a mixed-method design with a concurrent approach. A cross-sectional study was conducted to compare and examine the relationship between the outcomes of the structured oral examination (SOE) and the Diagnostic Thinking Inventory (DTI). Then, the qualitative method was used. A focus group discussion using a semi-structured interview guide with open-ended questions was conducted, then the verbatim transcript was subjected to thematic analysis. Results: There is an increase in SOE and DTI scores between second-year to fourth-year students. The diagnostic thinking domains and SOE are significantly correlated (r=0.302, 0.313, and 0.241 with p<0.05). The three primary themes from the qualitative analysis are perceptions regarding clinical reasoning, clinical reasoning activities, and the learning component. Conclusion Even if students are still studying throughout the COVID-19 pandemic, their clinical reasoning skills can improve. The clinical reasoning and diagnostic thinking skills of medical students increase as the length of the school year increases. Online case-based learning and assessment support the development of clinical reasoning skills. The skills are supported in their development by positive attitudes toward faculty, peers, case type, and prior knowledge.