Projection microstereolithography (PµSL) is a promising additive manufacturing technique due to its low cost, accuracy, speed, and also the diversity of the materials that it can use. Recently it has shown great potentials in various applications such as microfluidics, tissue engineering, micro-optics, biomedical microdevices, and so on. However, studies on PµSL are still ongoing in terms of the quality and accuracy of the construction process, which particularly affect the fabrication of complex 3D microstructures and make it attractive enough to be considered for commercial applications. In this paper, a compact LED-based PµSL 3D printer for the fabrication of 3D microstructures was developed, and the effective parameters that influence the quality of construction were thoroughly investigated and optimized. Accordingly, a customized optical system, including illumination optics and projection optics, was designed using optical engineering principles. This custom 3D printer was proposed for the PµSL process, which besides improving the quality of construction, led to the reduction of the size of the device, its cost-effectiveness, and the repeatability of its performance. To demonstrate the performance of the fabricated device, a variety of complex 3D microstructures such as porous, hollow, helical, and self-support microstructures were constructed. In addition, the repeatability of the device was assessed by fabricating microstructure arrays. The device performance showed that the lateral accuracy of printing was better than 5 μm, and the smallest thickness of the printed layer was 1 μm. Moreover, the maximum printable size of the device was 6.4 mm × 4 mm × 40 mm.