Synthetic FLAIR images are of lower quality than conventional FLAIR images. Here, we aimed to improve the synthetic FLAIR image quality using deep learning with pixel-by-pixel translation through conditional generative adversarial network training. Forty patients with MS were prospectively included and scanned to acquire synthetic MRI and conventional FLAIR images. Acquired data were divided into 30 training and 10 test datasets. Using deep learning, we improved the synthetic FLAIR image quality by generating FLAIR images that have contrast that is closer to that of conventional FLAIR images and fewer granular and swelling artifacts, while preserving the lesion contrast.