This book constitutes the refereed proceedings of the Joint 21st International Workshop on Formal Methods for Industrial Critical Systems and the 16th International Workshop on Automated Verification of Critical Systems, FMICS-AVoCS 2016, held in Pisa, Italy, in September 2016. The 11 full papers and 4 short papers presented together with one invited talk were carefully reviewed and selected from 24 submissions. They are organized in the following sections: automated verification techniques; model-based system analysis; and applications and case studies.