This paper focuses on automatic locking of tracking filters used in optical frequency transfer systems. General concept of such a system is briefly described and the problems with its automatic startup, originating in the use of the analog phase locked loop to filter weak, received signal, are discussed. A supervisory circuitry and algorithm to solve these problems is proposed. The frequency of the signal to be filtered is measured indirectly and the output frequency of the tracking filter is monitored. In the case of lack of synchronism (i:e: after the startup) a significant difference of these frequencies is measured and the supervisory algorithm forces the filter to tune into the right frequency and then allows it to synchronize. A system with the proposed solution was implemented and tested experimentally on a fiber optic link with high attenuation and multiple optical connectors. Transient signals during locking were recorded to investigate the system’s behavior in real environment. The system was evaluated in the link causing synchronization losses every 17 min on average. During measurements over 3 days, the whole system was synchronized for over 99.98% of time despite these difficult conditions.