Manual analysis of myocardial tissue mapping is time consuming. Deep learning has a potential to facilitate the analysis but requires big training datasets. In this study, a deep fully convolutional neural network, trained using native T1 mapping dataset, is used for T2 and extracellular volume (ECV) quantification based on transfer learning. We prospectively acquired T2 (401 patients) and ECV maps (381 patients) to access the network performance. Compared with the manually analyzed reference values, the transfer learning-based automated analysis platform shows good performance for myocardial T2 and ECV mapping. The platform has potential to fully automate myocardial tissue mapping.