A miniaturized pump to manipulate liquid flow in microchannels is the key component of microfluidic devices. Many researchers have demonstrated active microfluidic pumps, but most of them still required additional large peripherals to operate their micropumps. In addition, those micropumps were made of polymer materials so that their application may be limited to a variety of fields that require harsh conditions at high pressures and temperatures or organic solvents and acid/base. In this work, we present a 3D miniaturized magnetic-driven glass centrifugal pump for microfluidic devices. The pump consists of a volute structure and a 3D impeller integrated with two magnet disks of Φ1 mm. The 3D pump structure was 13 mm × 10.5 mm × 3 mm, and it was monolithically fabricated in a fused silica sheet by selective laser-induced etching (SLE) technology using a femtosecond laser. The pump operation requires only one motor rotating two magnets. It was Φ42 mm × 54 mm and powered by a battery. To align the shaft of the motor to the center of the 3D glass pump chip, a housing containing the motor and the chip was fabricated, and the overall size of the proposed micropump device was 95 mm × 70 mm × 75 mm. Compared with other miniaturized pumps, ours was more compact and portable. The output pressure of the fabricated micropump was between 215 Pa and 3104 Pa, and the volumetric flow rate range was 0.55 mL/min and 7.88 mL/min. The relationship between the motor RPM and the impeller RPM was analyzed, and the flow rate was able to be controlled by the RPM. With its portability, the proposed pump can be applied to produce an integrated and portable microfluidic device for point-of-care analysis.