The Mini-EUSO instrument is designed by the JEM-EUSO collaboration to pave the way for space-based observations of Extreme Energy Cosmic Rays (EECRs). To be placed inside the International Space Station (ISS) in early 2018, it is a small, UV (300 - 400 nm) telescope which will observe the Earth’s atmosphere with a spatial resolution of 6.11 km. Mini-EUSO is capable of detecting a wide variety of UV events such as cosmic ray signals, transient luminous events and meteors with a minimum time resolution of 2.5 μs. It will also be possible to detect space debris during twilight periods. The flight software is fully automated and takes advantage of the frequent day/night cycles of the ISS orbit and ancillary instruments with which Mini-EUSO is equipped in order to optimise the mission’s scientific output. The flight operations of Mini-EUSO are presented including the data acquisition, storage and transfer, astronaut interaction and predicted instrument duty cycle.