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.