Linear accelerator (LINAC) has been broadly used in various applications in recent years. For instance, the LINAC can produce X-rays and high-energy electrons, which are utilised in radiation therapy for medical purposes and also applied to fruit steriliser for exportation. At present, the prototype of the 6 MeV LINAC for fruit irradiation by using a magnetron radio frequency (RF) source has been developed at Synchrotron Light Research Institute (SLRI) in Nakhon Ratchasima, Thailand. The LINAC consists of several key sub-systems such as pulsed modulators both for electron gun and magnetron used to power the LINAC, magnetic guidance and beam diagnostic systems. All these have been integrated and worked in proper function to reach a proper and stable RF acceleration. Therefore, a timing system is required with well synchronisation for precise transfer of the clock and reference trigs to each sub-system. Furthermore, the low-cost in-house synchronous equipment has been built here for domestic researchers when they would like to apply this system to their work in the future; consequently, the FPGA-based system for real-time synchronisation has been created to achieve the sequences of the LINAC timing system. In this design, the Zybo Z7 development board from the Xilinx Zynq-7000 family is chosen, which integrates the programmable logic (PL) and processing system (PS) in the same chip. The experimental results are presented by the LINAC operation with synchronisation between a precise time and various delay times on both pulsed modulators, which the synchronous technique with accurate time demonstrates excellent performances leading to stable X-ray radiation for fruit irradiation with synchronous operation between the electron gun and magnetron.