This book constitutes the refereed proceedings of the 16th International Conference on Cryptology in Africa, AFRICACRYPT 2025, which took place in Rabat, Morocco in July 2025. The 21 full papers presented in this volume were carefully reviewed and selected from 45 submissions. They are grouped into the following topics: Homomorphic Encryption; Cryptanalysis of RSA; Cryptography Arithmetic; Side-channel Attacks; Designs; Cryptanalysis.