Based on a Mach-Zehnder intensity modulator, Bunch Arrival time Monitor (BAM) is a single-shot non-destructive multi-bunch diagnostic instrument, which measures the arrival time with <10 fs precision in the range of 10-200 pC at 100 Hz repetition rate. Being directly coupled to a length stabilized fiber optical link, it has intrinsically low drift (<10 fs/day) and is thus a useful instrument for the machine feedback. The overall monitor complexity demands the development of an extremely reliable control system that handles basic BAM operations. Two BAM prototypes were successfully used in the SwissFEL Injector Test Facility and further two are being presently commissioned at the SwissFEL. The system is very flexible. It provides a set of tools allowing one to implement a number of advanced control features such as tagging experimental data with a SwissFEL machine pulse number or embedding high level control applications into the process controllers (IOC). The paper presents the structure of the BAM control setup. The operational experience with this setup is also discussed.