Deep neural networks (DNNs) are phenomenally successful machine learning methods broadly applied to many different disciplines. However, as complex two-party computations, DNN inference using classical cryptographic methods cannot achieve unconditional security, raising concern on security risks of DNNs’ application to sensitive data in many domains. We overcome such a weakness by introducing a quantum-aided security approach. We build a quantum scheme for unconditionally secure DNN inference based on quantum oblivious transfer with an untrusted third party. Leveraging DNN’s noise tolerance, our approach enables complex DNN inference on comparatively low-fidelity quantum systems with limited quantum capacity. We validated our method using various applications with a five-bit real quantum computer and a quantum simulator. Both theoretical analyses and experimental results demonstrate that our approach manages to operate on existing quantum computers and achieve unconditional security with a negligible accuracy loss. This may open up new possibilities of quantum security methods for deep learning.