This work investigates the impact of the neural networks architecture when performing fingerprint recognition. Three networks are studied; a Triplet network and two Siamese networks. They are evaluated on datasets with specified amounts of relative translation between fingerprints. The results show that the Siamese model based on contrastive loss performed best in all evaluated metrics. Moreover, the results indicate that the network with a categorical scheme performed inferior to the other models, especially in recognizing images with high confidence. The Equal Error Rate (EER) of the best model ranged between 4%−11% which was on average 6.5 percentage points lower than the categorical schemed model. When increasing the translation between images, the networks were predominantly affected once the translation reached a fourth of the image. Our work concludes that architectures designed to cluster data have an advantage when designing an authentication system based on neural networks.