Background This case study in Makassar City, Indonesia aims to investigate the clinicians’ perceptions, including both satisfaction and barriers in using telemedicine in a large, established program which supported 3974 consultations in 2017. Methods A mixed methodology was used in this research utilizing a questionnaire with 12 questions, and semi-structured interviews. A purposeful sample of clinicians using the telemedicine system at the 39 primary care clinics in Makassar City were surveyed. A total of 100 clinicians participated in this study. All of them completed the questionnaires (76.9% response rate) and 15 of them were interviewed. Results The result showed that 78% of the clinicians were satisfied with the telemedicine system. In free text responses 69% said that telemedicine allowed quicker diagnosis and treatment, 47% said poor internet connectivity was a significant obstacle in using the system, and 40% suggested improvement to the infrastructure including internet connection and electricity. Conclusion Overall, the clinicians were satisfied with the system, with the main benefit of rendering the diagnosis faster and easier for patients. However, poor internet connectivity was indicated as the main barrier. Most of the clinicians suggested improving the infrastructure especially the internet network.