This book constitutes the refereed proceedings of the 13th European Workshop on Computer Performance Engineering, EPEW 2016, held in Chios, Greece, in October 2016. The 14 papers presented  together with 2 invited talks in this volume were carefully reviewed and selected from 25 submissions. The papers presented at the workshop reflect the diversity of modern performance engineering, with topics ranging from the analysis of queueing networks and stochastic processes, to performance analysis of computer systems and networks, and even modeling of human behavior.