This volume contains a record of some of the lectures and seminars delivered at the Second International School on Engineering Trustworthy Software Systems (SETSS 2016), held in March/April 2016 at Southwest University in Chongqing, China. The six contributions included in this volume provide an overview of leading-edge research in methods and tools for use in computer system engineering. They have been distilled from six courses and two seminars on topics such as: modelling and verification in event-B; parallel programming today; runtime verification; Java in the safety-critical domain; semantics of reactive systems; parameterized unit testing; formal reasoning about infinite data values; and Alan Turing and his remarkable achievements. The material is useful for postgraduate students, researchers, academics, and industrial engineers, who are interested in the theory and practice of methods and tools for the design and programming of trustworthy software systems.