Optical Coherence Tomography (OCT) is a high-resolution, non-invasive and contactless imaging technique based on optical interferometry. After the Time Domain (TD) and the Spatially Encoded Frequency Domain (SEFD), the Swept-Source (SS) OCT, also known as Time Encoded Frequency Domain (TEFD) OCT, is the latest technology available. It is based on a fast wavelength-sweeping of a narrow laser line over the bandwidth of the source. SWEEP TRIGGER and K-CLOCK signals are provided by the laser source and establish the time base for the overall system. Data acquisition and the two-dimensional scanning of the object of interest must be accurately synchronized after those signals. The proposed solution for the overall scanning/acquisition/sweeping synchronism is an integrated and dedicated FPGA-based control system that is being developed and will generate the automatic, programmable and flexible operation that will replace the present, manually adjustable, system. This way, complete reproducibility of experimental conditions will be obtained, along with the possibility of optimizing the galvanometer /mirrors control. This system is being built around a Xilinx XC6SLX45 FPGA and will be integrated in the already developed control software of the OCT system.