The two-volume set LNCS 15577 + 15578 constitutes the proceedings of the 16th International Workshop on Post-Quantum Cryptography, PQCrypto 2025, held in Taipei, Taiwan, during April 8-10, 2025. The 25 full papers presented in the proceedings were carefully selected and reviewed from 59 submissions. The papers have been organized in the following topical sections: Part I: Code-Based Cryptography; Multivariate Cryptography; Lattice-Based Cryptography. Part II: Isogeny-Based Cryptography; Cryptanalysis; Quantum Security; Side-Channel Attacks; Security Notions.