Internet of Things (IoT) connects various kinds of intelligent objects and devices using the internet to collect and exchange data. Nowadays, The IoT is used in diverse application domains, including the healthcare. In the healthcare domain, the IoT devices can collects patient data, and its forwards the data to the healthcare professionals can view it. The IoT devices are usually resource-constrained in terms of energy consumption, storage capacity, computational capability, and communication range, data aggregation techniques are used to reduce the communication overhead. However, in healthcare system using IoT, the heterogeneity of technologies, the large number of devices and systems, and the different types of users and roles create important challenges in terms of security. For that, the security and privacy aggregation of health data are very important aspects. In this paper, we propose a novel secure data aggregation scheme based on homomorphic primitives in IoT based healthcare systems, called “An Efficient and Privacy-Preserving Data Aggregation Scheme with authentication for IoT-Based Healthcare applications” (EPPDA). EPPDA is based the Verification and Authorization phase to verifying the legitimacy of the nodes wants to join the process of aggregation. EPPDA uses additive homomorphic encryption to protect data privacy and combines it with homomorphic MAC to check the data integrity. The security analysis and experimental results show that our proposed scheme guarantees data privacy, messages authenticity, and integrity, with lightweight communication overhead and computation.