Homomorphic Encryption (HE) based secure Neural Networks(NNs) inference is one of the most promising security solutions to emerging Machine Learning as a Service (MLaaS). In the HE-based MLaaS setting, a client encrypts the sensitive data, and uploads the encrypted data to the server that directly processes the encrypted data without decryption, and returns the encrypted result to the client. The clients' data privacy is preserved since only the client has the private key. Existing HE-enabled Neural Networks (HENNs), however, suffer from heavy computational overheads. The state-of-the-art HENNs adopt ciphertext packing techniques to reduce homomorphic multiplications by packing multiple messages into one single ciphertext. Nevertheless, rotations are required in these HENNs to implement the sum of the elements within the same ciphertext. We observed that HENNs have to pay significant computing overhead on rotations, and each of rotations is $\sim 10\times$ more expensive than homomorphic multiplications between ciphertext and plaintext. So the massive rotations have become a primary obstacle of efficient HENNs. In this paper, we propose a fast, frequency-domain deep neural network called Falcon, for fast inferences on encrypted data. Falcon includes a fast Homomorphic Discrete Fourier Transform (HDFT) using block-circulant matrices to homomorphically support spectral operations. We also propose several efficient methods to reduce inference latency, including Homomorphic Spectral Convolution and Homomorphic Spectral Fully Connected operations by combing the batched HE and block-circulant matrices. Our experimental results show Falcon achieves the state-of-the-art inference accuracy and reduces the inference latency by $45.45\%\sim 85.34\%$ over prior HENNs on MNIST and CIFAR-10.