A 250 MeV injector facility at PSI has been constructed to study the scientific and technological challenges of the SwissFEL project. Since in such pulsed machines in principle every beam can have different characteristics, due to varying machine parameters and/or conditions, it is very crucial to be able to acquire and distinguish control system data from one pulse to the next. In this paper we describe the technique we have developed to perform beam synchronous data acquisition at 100 Hz rate. This has been particularly challenging since it had to provide us with a reliable and real-time data acquisition method in a non real-time control system. We describe how this can be achieved by employing a powerful and flexible timing system with well defined interfaces to the control system.