Deep-learning based Super-Resolution (SR) methods have exhibited promising performance under non-blind setting where blur kernel is known; however, blur kernels of Low-Resolution (LR) images in different practical applications are usually unknown. It may lead to a significant performance drop when degradation process of training images deviates from that of real images. In this paper, we propose a novel blind SR framework to super-resolve LR images degraded by arbitrary blur kernel with accurate kernel estimation in frequency domain. To our best knowledge, this is the first deep learning method which conducts blur kernel estimation in frequency domain. Specifically, we first demonstrate that feature representation in frequency domain is more conducive for blur kernel reconstruction than in spatial domain. Next, we present a Spectrum-to-Kernel (S$2$K) network to estimate general blur kernels in diverse forms. We use a conditional GAN (CGAN) combined with SR-oriented optimization target to learn the end-to-end translation from degraded images' spectra to unknown kernels. Extensive experiments on both synthetic and real-world images demonstrate that our proposed method sufficiently reduces blur kernel estimation error, thus enables the off-the-shelf non-blind SR methods to work under blind setting effectively, and achieves superior performance over state-of-the-art blind SR methods, averagely by 1.39dB, 0.48dB (Gaussian kernels) and 6.15dB, 4.57dB (motion kernels) for scales $2\times$ and $4\times$ respectively.