Automated ranking of pre-trained Deep Neural Networks (DNNs) reduces the required time for selecting optimal pre-trained DNN and boost the classification performance in transfer learning. In this paper, we introduce a novel algorithm to rank pre-trained DNNs by applying a straightforward distance-based complexity measure named Separation Index (SI) to the target dataset. For this purpose, at first, a background about the SI is given and then the automated ranking algorithm is explained. In this algorithm, the SI is computed for the target dataset which passes from the feature extracting parts of pre-trained DNNs. Then, by descending sort of the computed SIs, the pre-trained DNNs are ranked, easily. In this ranking method, the best DNN makes maximum SI on the target dataset and a few pre-trained DNNs may be rejected in the case of their sufficiently low computed SIs. The efficiency of the proposed algorithm is evaluated by using three challenging datasets including Linnaeus 5, Breast Cancer Images, and COVID-CT. For the two first case studies, the results of the proposed algorithm exactly match with the ranking of the trained DNNs by the accuracy on the target dataset. For the third case study, despite using different preprocessing on the target data, the ranking of the algorithm has a high correlation with the ranking resulted from classification accuracy.