Single-photon light detection and ranging (LiDAR) has emerged as a strong candidate technology for active imaging applications. Benefiting from the single-photon sensitivity in detection, long-range active imaging can be realized with a low-power laser and a small-aperture transceiver. However, existing kilometer-range active imagers are bulky and have a long data acquisition time. Here we present a compact co-axial single-photon LiDAR system for kilometer-range 3D imaging. A fiber-based transceiver with a 2.5 cm effective aperture was employed to realize a robust and compact architecture, while a tailored temporal filtering approach guaranteed the high signal-to-noise level. Moreover, a micro-electro-mechanical system scanning mirror was adopted to achieve fast beam scanning. In experiment, high-resolution 3D images of different targets up to 12.8 km were acquired to demonstrate the long-range imaging capability. Furthermore, it exhibits the ability to achieve dynamic imaging at five frames per second over a distance of ∼1km. The results indicate potential in a variety of applications such as remote sensing and long-range target detection.