Micropumps are important components of advanced microfluidic systems. Here, polyimide (PI) as an advantageous structural material for flexible micropumps was focused on. This is because PI has many advantageous properties such as high thermal stability and superior mechanical strength. However, the difficulty in realizing an all-PI micropump lies in fabricating microstructures on PI film surfaces. In this paper, we present a novel all-PI micropump fabricated using hot embossing. The micropump had diffuser/nozzle valves and functioned by vibrating a 2-µm-thick PI diaphragm with alternating air pressures between 0 and 10 kPa at a frequency of 3 Hz. The height and diameter of the PI micropump chamber were 200 µm and 5 mm, respectively. The flow rate of water in the micropump was 34 µl/min. This micropump is suitable for flexible microfluidic systems.