The increasing concerns about data privacy and the stringent enforcement of data protection laws are placing growing pressure on organizations to secure large datasets. The challenge of ensuring data privacy becomes even more complex in the domains of Artificial Intelligence and Machine Learning due to their requirement for large amounts of data. While approaches like differential privacy and secure multi-party computation allow data to be used with some privacy guarantees, they often compromise data integrity or accessibility as a tradeoff. In contrast, when using encryption-based strategies, this is not the case. While basic encryption only protects data during transmission and storage, Homomorphic Encryption (HE) is able to preserve data privacy during its processing on a centralized server. Despite its advantages, the computational overhead HE introduces is notably challenging when integrated into Neural Networks (NNs), which are already computationally expensive. In this work, we present a framework called ENNigma, which is a Private Neural Network (PNN) that uses HE for data privacy preservation. Unlike some state-of-the-art approaches, ENNigma guarantees data security throughout every operation, maintaining this guarantee even if the server is compromised. The impact of this privacy preservation layer on the NN performance is minimal, with the only major drawback being its computational cost. Several optimizations were implemented to maximize the efficiency of ENNigma, leading to occasional computational time reduction above 50%. In the context of the Network Intrusion Detection System application domain, particularly within the sub-domain of Distributed Denial of Service attack detection, several models were developed and employed to assess ENNigma’s performance in a real-world scenario. These models demonstrated comparable performance to non-private NNs while also achiev ing the two-and-a-half-minute inference latency mark. This suggests that our framework is approaching a state where it can be effectively utilized in real-time applications. The key takeaway is that ENNigma represents a significant advancement in the field of PNN as it ensures data privacy with minimal impact on NN performance. While it is not yet ready for real-world deployment due to its computational complexity, this framework serves as a milestone toward realizing fully private and efficient NNs.