Background Multiple Sclerosis (MS), is a chronic idiopathic demyelinating disorder of the CNS. Imaging plays a central role in diagnosis and monitoring. Monitoring for progression however, can be repetitive for neuroradiologists, and this has led to interest in automated lesion detection. Simultaneously, in the computer science field of Remote Sensing, Change Detection (CD), the identification of change between co-registered images at different times, has been disrupted by the emergence of Vision Transformers. CD offers an alternative to semantic segmentation leveraging the temporal information in the data. Methods In this retrospective study with external validation we reframe the clinical radiology task of new lesion identification as a CD problem. Consecutive patients who had MRI studies for MS at our institution between 2019 and 2022 were reviewed and those with new lesion(s) were included. External data was obtained from the MSSEG2 challenge and OpenMS. Multiple CD models, and a novel model (NeUFormer), were trained and tested. Results were analysed on both paired slices and at the patient level. Expected Cost (EC) and F2 were independently and prospectively chosen as our primary evaluation metrics. For external data we report DICE and F1 to allow for comparison with existing data. For each test set 1000 bootstrapping simulations were performed by sampling 10 patient samples with replacement giving a non parametric estimate of the confidence interval. Wilcoxon statistics were calculated to test for significance. Findings 43,440 MR images were included for analysis (21,720 pairs). The internal set comprised of 170 patients (110 for training, 30 for tuning, 30 testing) with 120 females and 50 males, average age of 42 (range 21,74). 60 (40 + 20) patients were included for external validation. In the CD experiments (2D) our proposed NeuFormer model achieved the best (lowest) Expected Cost (EC) (p=0.0095), the best F2 and second best DICE (p<0.0001). At the patient level our NeUFormer model had the joint highest number of True Positive lesions, and lowest number of False negatives (p<0.002). For CD on external data, NeUFormer achieved the highest DICE on both datasets (p<0.0001). NeUFormer had the lowest or joint lowest number of False Positives on external data (p<0.0001 in all cases). Interpretation Reformulating new lesion identification as a CD problem allows the use of new techniques and methods of evaluation. We introduce a novel Siamese U-Transformer, NeUFormer, which combines concepts from U-Net, Siamese Networks, and vision transformers to create a model with improved small lesion detection and the consistently best EC. Its ability to increase detection of small lesions, balanced with relatively few false positives, and superior generalisability has the potential to greatly impact the field of the identification of radiologic progression of MS with AI.