Hyperspectral imaging systems that use multispectral filter arrays (MSFA) capture only one spectral component in each pixel. Hyperspectral demosaicing is used to recover the non-measured components. While deep learning methods have shown promise in this area, they still suffer from several challenges, including limited modeling of non-local dependencies, lack of consideration of the periodic MSFA pattern that could be linked to periodic artifacts, and difficulty in recovering high-frequency details. To address these challenges, this paper proposes a novel de-mosaicing framework, the MSFA-frequency-aware Transformer network (FDM-Net). FDM-Net integrates a novel MSFA-frequency-aware multi-head self-attention mechanism (MaFormer) and a filter-based Fourier zero-padding method to reconstruct high pass components with greater difficulty and low pass components with relative ease, separately. The advantage of Maformer is that it can leverage the MSFA information and non-local dependencies present in the data. Additionally, we introduce a joint spatial and frequency loss to transfer MSFA information and enhance training on frequency components that are hard to recover. Our experimental results demonstrate that FDM-Net outperforms state-of-the-art methods with 6dB PSNR, and reconstructs high-fidelity details successfully.