Background: Increasing attention is being paid to improve the quality of life of patients with rare diseases in China. However, we are currently unaware of the problems encountered in the medical services of rare diseases from the viewpoints of doctors and patients. This study addressed the differences in the perceived barriers of diagnosis and treatments for rare diseases between doctors and patients in China. Methods: Two independent cross-sectional surveys on the perception of Chinese doctors' and patients' experiences with rare diseases were launched online between January and February 2018. A non-probability, convenience sampling method was employed to recruit participants. Results: In all, 45 rare diseases were reported by 139 doctors and 1853 patients. Patients with rare diseases faced significantly more difficulties in receiving accurate diagnosis (72.0%) and accessing information related to diagnosis and treatment (77.3%) as compared with doctors (34.5% and 40.3%, p < 0.0001, respectively). Specially, patients felt more difficulties than doctors in obtaining sustainable treatment for rare diseases (84.3% vs. 49.6%, p < 0.001). A higher percentage of patients (58.7%) than that of doctors (39.1%) had concerns in terms of the affordability of drugs. Further, 66.3% patients claimed that the drugs used to treat their conditions were not covered by their current medical insurances, whereas only 21.6% for doctors (p < 0.0001). Moreover, 35.3% of doctors responded that they recommended patients to visit the specialist they knew or were acquainted with, whereas 30.0% of patients said that their doctors chose to treat them based on their past experiences (p < 0.001). Conclusion: The perceived experience of patients with regard to diagnosis and treatment was significantly different from that of doctors. An integrated medical service platform should be established to facilitate better communication and mutual understanding of rare diseases between patients and doctors.