Sub-pixel micro-scanning is a relatively simple way of utilizing a low pixel count sensor to better realise the resolution capabilities of a given objective lens. This technique accomplishes this by shifting the sensor array in the image plane through distances less than the pixel dimensions, gathering multiple images from different viewpoints that can be combined into a single, more detailed image. Applying this technique to a single-photon counting light detection and ranging (LiDAR) system allows for improved depth and intensity image reconstruction. Time-correlated single-photon counting (TCSPC) allowed for time-of-flight data to be measured, and the high-sensitivity and picosecond timing resolution this provided enabled us to create high-resolution intensity images and depth maps from distant targets whilst maintaining low average optical output power levels. The LiDAR system operated at a wavelength of 1550 nm, and used a pulsed fiber laser source for flood-illumination of the target scene. The detector was a 32 × 32 InGaAs/InP single-photon avalanche diode detector array mounted on precision translation stages. Operating in the short-wave infrared meant that the system could work at long range in daylight conditions, as the effect of solar background is reduced compared to shorter wavelengths and atmospheric transmission was relatively high. This paper presents depth and intensity profiles taken at a target range of approximately 325 m from the system location. The transceiver system operated at eye-safe, low average optical output power levels, typically below 5 mW.