HYSYS was first conceived and created by the Canadian company Hyprotech, founded by researchers from the University of Calgary. The HYSYS Version 1.1 Reference Volume was published in 1996.
In May 2002, AspenTech acquired Hyprotech, including HYSYS. Following a 2004 ruling by the United States Federal Trade Commission, AspenTech was forced to divest its Hyprotech assets, including HYSYS source code, ultimately selling these to Honeywell. Honeywell was also able to hire a number of HYSYS developers, ultimately mobilizing these resources to produce UniSim. The divestment agreement specified that Aspentech would retain rights to market and develop most Hyprotech products (including HYSYS) royalty-free. As of late 2016, AspenTech continues to produce HYSYS.