Terahertz time-domain spectroscopy systems driven by monolithic mode-locked laser diodes (MLLDs) exhibit bandwidths exceeding 1 THz and a peak dynamic range that can compete with other state-of-the-art systems. Their main difference compared to fiber-laser-driven systems is their ultra-high repetition rate of typically dozens of GHz. This makes them interesting for applications where the length of the terahertz path may not be precisely known and it enables the use of a very short and potentially fast optical delay unit. However, the phase accuracy of the system is limited by the accuracy with which the delay axes of subsequent measurements are synchronized. In this work, we utilize an all-fiber approach that uses the optical signal from the MLLD in a Mach–Zehnder interferometer to generate a reference signal that we use to synchronize the detected terahertz signals. We demonstrate transmission-mode thickness measurements of stacked layers of 17μm thick low-density polyethylene (LDPE) films.