We propose a system time synchronization method between ARM-based embedded Linux systems. The master Linux with reference clock sends its own system time to the slave Linux via Transmission Control Protocol communication along with a general-purpose input/output (GPIO) signal, and then the slave Linux corrects its own system time by the difference between its own system time at receiving the GPIO signal and the received reference time. The synchronization performance is significantly improved by compensating for the GPIO signal detection latency and the system time acquisition and setting latencies in Linux. These latencies are precisely measured by exploiting the function of Cycle Counter register in ARM coprocessor. Extensive experiments are performed with two ARM-based embedded Linux systems, and the results demonstrate the validity and performance of the proposed synchronization method.