JPL is developing the Lunar Flashlight (LF) CubeSat mission, a 6U 14 kg spacecraft whose objective is to demonstrate new technology and measure potential surface water ice deposits in the permanently shadowed region (PSR) of the moon in preparation of future possible human lunar exploration. This mission will become the first interplanetary CubeSat to orbit the Moon. It uses a new green propulsion system as well as an instrument with spectrally tuned IR laser technology to search for volatiles in a specific region of the moon. The Guidance, Navigation and Control (GNC) system is crucial for delivering the spacecraft from Earth into Lunar orbit and supporting scientific measurements. Due to the challenging lunar orbit insertion and high tip off rate out of launch vehicle's dispenser, the initial design concept using solar sail propulsion accompanied with small commercial-on-the-shelf (COTS) reaction wheels was abandoned mid-course and replaced by a green propulsion system along with larger reaction wheels, both newly developed for LF. However, using thrusters for the small CubeSat created an additional challenge of controlling the spacecraft attitude. The story of the GNC system development, qualifications, technical challenges encountered, and lessons learned are discussed in this paper.