In 2007, he received the W. Wallace McDowell Award, the highest technical honor awarded by the IEEE Computer Society, for his pioneering contributions to theory, technique, and practice of pattern recognition, computer vision, and biometric recognition systems.

He also received best paper awards from the IEEE Transactions on Neural Networks (1996) and the Pattern Recognition journal (1987, 1991, and 2005).

[6] He served as a member of the U.S. National Academies panels on Information Technology, Whither Biometrics and Improvised Explosive Devices (IED).

[7] Based on his Google Scholar profile, he had an h-index of 200 in 2020, which was the highest among computer scientists identified in a survey published by UCLA at the time,[8] however he was since surpassed by Yoshua Bengio, a researcher of similar subjects (neural networks and deep learning for artificial intelligence).

[11] Anil Jain was conferred a doctorate honoris causa by the Hong Kong University of Science and Technology in 2021 and by the Universidad Autónoma de Madrid in 2018.