Iris is one of the common biometrics used for identity authentication. It has the potential to recognize persons with a high degree of assurance. Extracting effective features is the most important stage in the iris recognition system. Different features have been used to perform iris recognition system. A lot of them are based on hand-crafted features designed by biometrics experts. According to the achievement of deep learning in object recognition problems, the features learned by the Convolutional Neural Network (CNN) have gained great attention to be used in the iris recognition system. In this paper, we proposed an effective iris recognition system by using transfer learning with Convolutional Neural Networks. The proposed system is implemented by fine-tuning a pre-trained convolutional neural network (VGG-16) for features extracting and classification. The performance of the iris recognition system is tested on four public databases IITD, iris databases CASIA-Iris-V1, CASIA-Iris-thousand and, CASIA-Iris-Interval. The results show that the proposed system is achieved a very high accuracy rate.