The escalating threat and impact of network-based attacks necessitate innovative intrusion detection systems. Machine learning has shown promise, with recent strides in quantum machine learning offering new avenues. However, the potential of quantum computing is tempered by challenges in current noisy intermediate-scale quantum era machines. In this article, we explore quantum neural networks (QNNs) for intrusion detection, optimizing their performance within current quantum computing limitations. Our approach includes efficient classical feature encoding, QNN classifier selection, and performance tuning leveraging current quantum computational power. This study culminates in an optimized multilayered QNN architecture for network intrusion detection. A small version of the proposed architecture was implemented on IonQ’s Aria-1 quantum computer, achieving a notable 0.86 F1 score using the NF-UNSW-NB15 dataset. In addition, we introduce a novel metric, certainty factor, laying the foundation for future integration of uncertainty measures in quantum classification outputs. Moreover, this factor is used to predict the noise susceptibility of our quantum binary classification system.