Purpose: A coincidence detector is an essential unit to acquire distribution of radioisotopes in positron emission tomography (PET) systems. The coincidence pairs rapidly increase as the number of detector modules increase. To make this system compact, flexible, and conveniently controllable, a field programmable gated array (FPGA)-based coincidence detector was developed. Methods: The unit targeted PET systems have eight detector modules. The coincidence detector module needs veto function for controlling the data transfer rate of the output signal because the output is connected to the band-limited ADC and data transfer unit. The coincidence detector module has eight inputs connected to the detector modules, one coincidence output signal connected to the trigger input of the ADC, and three control signals for setting system parameters, such as the coincidence window time, output pulse length, and veto time. Results: The performance of the unit was restricted by system clock frequency. The maximum clock frequency was 250 MHz when the unit was implemented to XILINX Spartan 3 FPGA. The unit had a minimum 2 ns of coincidence timing window when it runs in the double data rate (DDR) mode. The unit was also applied to PET image acquisition and the PET/CT and PET/MR images were successfully acquired. Conclusions: The coincidence unit developed in this study was useful for PET image acquisition with PMT- and SiPM-based PET prototypes. The unit can be easily extended to larger systems that have many more detector modules without extra components.