With the spread of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) disease and its potential risks for vulnerable groups such as the elderly with chronic diseases, telehealth appointments gained more attention around the world. However, using such a system brought about challenges to patients and service providers that need to be addressed by policymakers for system improvement. The present study was conducted with the aim of investigating the challenges of the telephone consultation program, which was run by the Social Security Insurance Organization of Iran during the epidemic of SARS-CoV-2. This qualitative study was conducted through semi-structured interviews with physicians who participated in the program, using a purposive sampling approach. The interviews were recorded, transcribed verbatim, and analyzed through conventional content analysis by ATLAS.ti9 software. Based on the results of the qualitative content analysis, the challenges in three categories, including program development, implementation, and evaluation and monitoring, and with 10 themes (planning challenges, infrastructure provision, education and culture building, legal issues, motivational mechanisms, effective communication, efficiency, and effectiveness of care, organization, monitoring, and evaluation) and 26 sub-themes were extracted. Telephone appointments allow medical centers to serve some patients better. However, properly implementing the telephone consultation program requires better planning, training, appropriate infrastructure, and continuous evaluation and improvement of processes.