In this study, we describe the development of a compact NIR multispectral imaging sensor for use in glare-free NIR color fundus cameras. Integrating NIR technology into a fundus camera offers significant advantages over conventional RGB imaging using visible illumination, as it enables the glare-free capture of fundus images with minimal patient discomfort. The specifications necessary for a glare-free NIR color fundus camera were evaluated on the basis of factors such as pixel pitch size, pixel array layout, and multilayer interference filter design, in accordance with the camera’s intended purpose. While multilayer interference filters were deposited on a glass substrate and bonded with the sensor chip in a 7.5 μm pixel pitch in a previous study, we propose an NIR multispectral imaging sensor directly depositing the interference filters on the wafer in a narrower 4 μm pixel pitch. In addition, the fabrication process for directly depositing NIR multispectral filters on the sensor wafer was proposed. The fabricated NIR multispectral imaging sensor was analyzed against the intended design. Finally, an NIR multispectral imaging sensor was installed on a glare-free NIR color fundus camera, and it was confirmed that the resulting camera is capable of providing medically relevant and meaningful information.