In this work, 40 × 40 μm2 blue InGaN micro-light-emitting diodes (μLEDs) with transparent and vertical package was first demonstrated by using either double-side polished zinc oxide (ZnO) or sapphire substrate as a transparent submount. The performance of the vertical and conventional packages was compared, where the devices packaged vertically resulted in smaller blueshift in peak wavelength with increasing drive current due to the higher junction temperature. Moreover, devices packaged vertically with the sapphire submount offered 19% and 32% greater light output power at 20 and 100 A cm−2, respectively, and 18% improvement in maximum external quantum efficiency (EQE) than devices with conventional package. Finally, the peak EQE of 58% was achieved from the μLED packaged vertically using a sapphire submount.