This medical image segmentation plays a fundamental role in the diagnosis of diseases related to the correct identification of internal structures and pathological regions in different imaging modalities. The conventional fuzzy-based segmentation approaches, though quite useful, still have some drawbacks regarding handling uncertainty, parameter optimization, and high accuracy of segmentation with diverse datasets. Because of these facts, it generally leads to poor segmentations, which can give less reliability to the clinical decisions. In addition, the paper is going to propose a model, FTra-UNet, with advanced segmentation of medical images by incorporating fuzzy logic and transformer-based deep learning. The model would take complete leverage of the strengths of FIS concerning the handling of uncertainties in segmentation. Besides, it integrates SSHOp optimization technique to fine-tune the weights learned by the model to ensure improvement in adaptability and precision. These integrated techniques ensure faster convergence rates and higher accuracy of segmentation compared to state-of-the-art traditional methods. The proposed FTra-UNet is tested on BRATS, CT lung, and dermoscopy image datasets and ensures exceptional results in segmentation accuracy, precision, and robustness. Experimental results confirm that FTra-UNet yields consistent, reliable segmentation outcomes from a practical clinical application perspective. The architecture and implementation of the model, with the uncertainty handled by FIS and the learning parameters optimization handled by the SSHOp method, increase the power of this model in segmenting medical images.