Fluorescence imaging in the brain of freely behaving mice is challenging due to severe miniaturization constraints. In particular, the ability to image a large field of view at high temporal resolution and with efficient out-of-focus background rejection still raises technical difficulties. Here, we present a novel fiberscope system that provides fast (up to 200 Hz) background-free fluorescence imaging in freely behaving mice over a field of view of diameter 230 μm. The fiberscope is composed of a custom-made multipoint-scanning confocal microscope coupled to the animal with an image guide and a micro-objective. By simultaneously registering a multipoint-scanning confocal image and a conventional widefield image, we subtracted the residual out-of-focus background and provided a background-free confocal image. Illumination and detection pinholes were created using a digital micromirror device, providing high adaptability to the sample structure and imaging conditions. Using this novel imaging tool, we demonstrated fast fluorescence imaging of microvasculature up to 120 μm deep in the mouse cortex, with an out-of-focus background reduced by two orders of magnitude compared with widefield microscopy. Taking advantage of the high acquisition rate (200 Hz), we measured red blood cell velocity in the cortical microvasculature and showed an increase in awake, unrestrained mice compared with anaesthetized animals.