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Background and Purpose: The development of Magnetic Resonance Imaging (MRI)-only Radiotherapy (RT) represents a significant advancement in the field. This study introduces a Deep Learning (DL) algorithm designed to quickly generate synthetic CT (sCT) images from low-field MR images in the brain, an area not yet explored. Methods: Fifty-six patients were divided into training (32), validation (8), and test (16) groups. A conditional Generative Adversarial Network (cGAN) was trained on pre-processed axial paired images. sCTs were validated using mean absolute error (MAE) and mean error (ME) calculated within the patient body. Intensity Modulated Radiation Therapy (IMRT) plans were optimised on simulation MRI and calculated considering sCT and original CT as electron density (ED) map. Dose distributions using sCT and CT were compared using global gamma analysis at different tolerance criteria (2 %/2mm and 3 %/3mm) and evaluating the difference in estimating different Dose Volume Histogram (DVH) parameters for target and organs at risk (OARs). Results: The network generated sCTs of each single patient in less than two minutes (mean time = 103 ± 41 s). For test patients, the MAE was 62.1 ± 17.7 HU, and the ME was −7.3 ± 13.4 HU. Dose parameters on sCTs were within 0.5 Gy of those on original CTs. Gamma passing rates 2 %/2mm, and 3 %/3mm criteria were 99.5 %±0.5 %, and 99.7 %±0.3 %, respectively. Conclusion: The proposed DL algorithm generates in less than 2 min accurate sCT images in the brain for online adaptive radiotherapy, potentially eliminating the need for CT simulation in MR-only workflows for brain treatments.