Background Deep‐learning is widely used for lesion classification. However, in the clinic patient data often has missing images. Purpose To evaluate the use of generated, duplicate and empty(black) images for replacing missing MRI data in AI brain tumor classification tasks. Study Type Retrospective. Population 224 patients (local‐dataset; low‐grade‐glioma (LGG) = 37, high‐grade‐glioma (HGG) = 187) and 335 patients (public‐dataset (BraTS); LGG = 76, HGG = 259). The local‐dataset was divided into training (64), validation (16), and internal‐test‐data (20), while the public‐dataset was an independent test‐set. Field Strength/Sequence T1WI, T1WI+C, T2WI, and FLAIR images (1.5T/3.0T‐MR), obtained from different suppliers. Assessment Three image‐to‐image translation generative‐adversarial‐network (Pix2Pix‐GAN) models were trained on the local‐dataset, to generate T1WI, T2WI, and FLAIR images. The rating‐and‐preference‐judgment assessment was performed by three human‐readers (radiologist (MD) and two MRI‐technicians). Resnet152 was used for classification, and inference was performed on both datasets, with baseline input, and with missing data replaced by 1) generated images; 2) duplication of existing images; and 3) black images. Statistical Tests The similarity between the generated and the original images was evaluated using the peak‐signal‐to‐noise‐ratio (PSNR) and the structural‐similarity‐index‐measure (SSIM). Classification results were evaluated using accuracy, F1‐score and the Kolmogorov–Smirnov test and distance. Results For baseline‐state, the classification model reached to accuracy = 0.93,0.82 on the local and public‐datasets. For the missing‐data methods, high similarity was obtained between the generated and the original images with mean PSNR = 35.65,32.94 and SSIM = 0.87,0.91 on the local and public‐datasets; 39% of the generated‐images were labeled as real images by the human‐readers. The classification model using generated‐images to replace missing images produced the highest results with mean accuracy = 0.91,0.82 compared to 0.85,0.79 for duplicated and 0.77,0.68 for use of black images; Data Conclusion The feasibility for inference classification model on an MRI dataset with missing images using the Pix2pix‐GAN generated images, was shown. The stability and generalization ability of the model was demonstrated by producing consistent results on two independent datasets. Level of Evidence 3 Technical Efficacy Stage 5