Brain ultrasound has attracted great attention recently due to its noninvasive treatment function for brain diseases. However, ultrasound is still difficult to pass through an intact skull. Phase correction is recognized as an effective method for skull compensation. Half-wavelength pitch transducer is important for the phase correction and, hence, thousands of elements array is required to cover large area human tissue. The clock synchronization between elements is crucial for the phase correction; however, the traditional clock scheme which is designed for 128- or 256-element system is not suitable for thousands of elements. In addition, the clock scheme needs to be magnetic resonance imaging (MRI) compatible since MRI-guided intervention is becoming a routine operation for the brain ultrasound. This study is the first to propose an optical fiber-based clock synchronization method for MRI-guided ultrasound array system. The optical fiber not only distributes the clock but also sets up a link to transmit the data for ultrasound beamformer. The link is full-duplex so both the clock and the data can be transmitted and received simultaneously. The precision of clock synchronization is less than 557 ps when using 50 MHz clock, and the period jitter of the clock is less than 10 ps (rms). Multiple 128- or 256-channel ultrasonic systems can be synchronized, and the error between the channels can be less than 10 ns when using 1-MHz ultrasound transducer. The system can work in an MRI scanning room and communicate with a console via only one fiber. In vivo primate animal study has been achieved, and it has been proven that the proposed clock scheme is suitable for MRI-guided large-scale ultrasound array system.