Sub-micron faculae (light spots) at the single-photon level have important applications in many fields. This report demonstrates a method for measuring facula size at the sub-micron single-photon level indirectly. The developed method utilizes Silicon Photomultipliers (SiPMs) as the single-photon response detectors, combined with a nano-positioning stage. The approach involves one- or two-dimensional space scanning and a deconvolution operation, which enable evaluations of the size and spatial distribution of focused facula in a single-photon-level pulsed laser. The results indicate that the average full width at half maximum of the faculae is about 0.66 µm, which is close to the nominal resolution of the objective lens of the microscope (0.42 µm). The proposed method has two key advantages: (1) it can measure sub-micron facula at the single-photon level, and (2) the sub-micron facula can easily be aligned with the detector because the array area of the avalanche photodiode cells in SiPM is usually larger than one square millimeter, and there is no need to put an optical slit, knife edge, or pinhole in front of the detector. The method described herein is applicable in weak light facula detection related fields.