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Precise automated delineation of post-operative gross tumor volume in glioblastoma cases is challenging and time-consuming owing to the presence of edema and the deformed brain tissue resulting from the surgical tumor resection. To develop a model for automated delineation of post-operative gross tumor volumes in glioblastoma, we proposed a novel 3D double pocket U-Net architecture that has two parallel pocket U-Nets. Both U-Nets were trained simultaneously with two different subsets of MRI sequences and the output from the models was combined to do the final prediction. We strategically combined the MRI input sequences (T1, T2, T1C, FL) for model training to achieve improved segmentation accuracy. The dataset comprised 82 post-operative studies collected from 23 glioblastoma patients who underwent maximal safe tumor resection. All had gross tumor volume (GTV) segmentations performed by human experts, and these were used as a reference standard. The results of 3D double pocket U-Net were compared with baseline 3D pocket U-Net models and the ensemble of 3D pocket U-Net models. All the models were evaluated with fivefold cross-validation in terms of the Dice similarity coefficient and Hausdorff distance. Our proposed double U-Net model trained with input sequences [T1, T1C, FL + T2, T1C] achieved a better mean Dice score of 0.8585 and Hausdorff distance of 4.1942 compared to all the baseline models and ensemble models trained. The presence of infiltrating tumors and vasogenic edema in the post-operative MRI scans tends to reduce segmentation accuracy when considering the MRI sequences T1, T2, T1C, and FL together for model training. The double U-Net approach of combining subsets of the MRI sequences as distinct inputs for model training improves segmentation accuracy by 7% when compared with the conventional method of model training with all four sequences.