Perception has recently been highlighted as a critical determinant for participation in clinical trials (CTs) among cancer patients. We evaluated cancer patients' current perceptions of CTs using the PARTAKE questionnaires, focusing on differences between patients with common and rare cancers. From November 2015 to May 2017, we prospectively surveyed patients who had received anti-cancer treatment at Asan Medical Center. Among 333 respondents, 70.9% had common and 29.1% had rare cancers. In the cohort, 87.7% of patients with common cancers and 75.3% of patients with rare cancers answered that they heard of and knew about CTs. However, willingness to participate in CTs was expressed only in approximately 56% of patients, although it was significantly associated with awareness and perception. Surprisingly, patients with rare cancers when compared with patients with common cancers showed significantly lower levels of awareness and perception (64.2% vs 79.9%, p = 0.003 and 77.3% vs 91.9%, p < 0.001), and consequently less willingness to participate in CTs (47.4% vs 58.9%, p = 0.06). In addition, cancer patients still harbored fear and concerns about safety and reward of CTs, and demonstrated substantial lack of knowledge about the voluntary nature of CTs, which was more obvious in patients with rare cancers. We identified relatively modest willingness of cancer patients to participate in CTs regardless of generally favorable perception. These findings are highlighted by the more negative perception of CTs among patients with rare cancers relative to those with common cancers. Further education and encouragement by research and public entities seem essential to improve motivation of CTs in cancer patients beyond good perception, especially for patients with rare cancers.