From 2010 to 2012 the Large Hadron Collider (LHC) operated at a centre-of-mass energy of 7 TeV and 8 TeV, colliding bunches of particles every 50 ns. During operation, the ATLAS trigger system has performed efficiently contributing to important results, including the discovery of the Higgs boson in 2012. The LHC restarted in 2015 and will operate for four years at a center of mass energy of 13 TeV and bunch crossing of 50 ns and 25 ns. These running conditions result in the mean number of overlapping proton-proton interactions per bunch crossing increasing from 20 to 60. The Fast Tracker (FTK) system is designed to deliver full event track reconstruction for all tracks with transverse momentum above 1 GeV at a Level-1 rate of 100 kHz with an average latency below 100 microseconds. This will allow the trigger to utilize tracking information from the entire detector at an earlier event selection stage than ever before, allowing for more efficient event rejection. To achieve this goal the system uses a parallel architecture, with algorithms designed to exploit the computing power of custom Associative Memory chips, and modern Field Programmable Gate Arrays. A partial FTK system has been built in 2016, and additional production is ongoing. The system is currently under commissioning. The functionality of the FTK system as well as an overview of the installation and commissioning status are described.