The GRAINE project observes cosmic gamma-rays, using a balloon-borne emulsion-film-based telescope in the sub-GeV/GeV energy band. We reported in our previous balloon experiment in 2018, GRAINE2018, the detection of the known brightest source, Vela pulsar, with the highest angular resolution ever reported in an energy range of >80MeV. However, the emulsion scanning system used in the experiment was designed to achieve a high-speed scanning, and it was not accurate enough to ensure the optimum spatial resolution of the emulsion film and limited the performance. Here, we report a new high-precision scanning system that can be used to greatly improve the observation result of GRAINE2018 and also be employed in future experiments. The scanning system involves a new algorithm that recognizes each silver grain on an emulsion film and is capable of measuring tracks with a positional resolution for the passing points of tracks of almost the same as the intrinsic resolution of nuclear emulsion film (∼70 nm). This resolution is approximately one order of magnitude smaller than that obtained with the high-speed scanning system. With this scanning system, an angular resolution for gamma-rays of 0.1° at 1GeV is expected to be achieved. Furthermore, we successfully combine the new high-precision scanning system with the existing high-speed scanning system, enabling the high-speed and high-precision measurements. Employing these techniques, we reanalyze the gamma-ray events detected previously by only the high-speed scanning system in GRAINE2018 and obtain an about three times higher angular resolution (0.22°) in the 500–700MeV energy range. Adopting this technique in future observations may provide new insights into the gamma-ray emission from the Galactic center region and may realize polarization measurements of high-energy cosmic gamma-rays.