Background: Deep learning (DL) could predict isocitrate dehydrogenase (IDH) mutation status from MRIs. Yet, previous work focused on CNNs with refined tumor segmentation. To bridge the gap, this study aimed to evaluate the feasibility of developing a Transformer-based network to predict the IDH mutation status free of refined tumor segmentation. Methods: A total of 493 glioma patients were recruited from two independent institutions for model development (TCIA; N = 259) and external test (AHXZ; N = 234). IDH mutation status was predicted directly from T2 images with a Swin Transformer and conventional ResNet. Furthermore, to investigate the necessity of refined tumor segmentation, seven strategies for the model input image were explored: (i) whole tumor slice; (ii–iii) tumor mask and/or not edema; (iv–vii) tumor bounding box of 0.8, 1.0, 1.2, 1.5 times. Performance comparison was made among the networks of different architectures along with different image input strategies, using area under the curve (AUC) and accuracy (ACC). Finally, to further boost the performance, a hybrid model was built by incorporating the images with clinical features. Results: With the seven proposed input strategies, seven Swin Transformer models and seven ResNet models were built, respectively. Based on the seven Swin Transformer models, an averaged AUC of 0.965 (internal test) and 0.842 (external test) were achieved, outperforming 0.922 and 0.805 resulting from the seven ResNet models, respectively. When a bounding box of 1.0 times was used, Swin Transformer (AUC = 0.868, ACC = 80.7%), achieved the best results against the one that used tumor segmentation (Tumor + Edema, AUC = 0.862, ACC = 78.5%). The hybrid model that integrated age and location features into images yielded improved performance (AUC = 0.878, Accuracy = 82.0%) over the model that used images only. Conclusions: Swin Transformer outperforms the CNN-based ResNet in IDH prediction. Using bounding box input images benefits the DL networks in IDH prediction and makes the IDH prediction free of refined glioma segmentation feasible.