Referral of cases from primary to secondary care in the Brazilian public healthcare system is one of the most important issues to be tackled. Telehealth strategies have been shown effective in avoiding unnecessary referrals. The objective of this study was to estimate cost per referred case by a remotely operated referral management system to further inform the decision making on the topic. Analysis of cost by applying time-driven activity-based costing. Cost analyses included comparisons between medical specialties, localities for which referrals were being conducted, and periods of time. Cost per referred case across localities ranged from R$ 5.70 to R$ 8.29. Cost per referred case across medical specialties ranged from R$ 1.85 to R$ 8.56. Strategies to optimize the management of referral cases to specialized care in public healthcare systems are still needed. Telehealth strategies may be advantageous, with cost estimates across localities ranging from R$ 5.70 to R$ 8.29, with additional observed variability related to the type of medical specialty.