The Ninkasi Brewing Company formed in 2006 in Eugene, Oregon.

Named after the Sumerian goddess of fermentation, Ninkasi Brewing Company was founded in 2006 by Jamie Floyd and Nikos Ridge. The first beer they produced was Total Domination IPA. The company's headquarters are in Eugene, Oregon's Whiteaker neighborhood.

Nikos Ridge was born and raised in Eugene, and moved to Manhattan in 1999, where he worked in finance; he moved back to Eugene in 2004. Jamie Floyd was born in Livermore and raised in Cupertino, California. He moved to attend the University of Oregon in 1990 and brewed his first batch of homebrew, in the kitchen of a campus co-op called The Lorax. In 2005, Floyd began working as a kitchen manager and assistant brewer at Steelhead Brewery in Eugene, where Teri Fahrendorf was the head brewer; after Fahrendorf left he became head brewer. Ridge and Floyd met in Eugene and in 2006 made their first batch of beer together: Total Domination IPA. The following six months, they continued to brew on a 15-barrel brewhouse located in a German restaurant in Springfield, Oregon.

In 2007, Ninkasi Brewing Company moved to its current location in Eugene’s Whiteaker neighborhood. By 2011, it was the fastest growing craft brewery in the United States and in 2020, was ranked as the 33rd largest craft brewery. The brewery produces year-round Flagship Series beers, a rotating Seasonal Release Series, Special Release Series beers, and Rare & Delicious (R&D) small-batch releases.

Ninkasi Brewing Company set out with the mission "to Perpetuate Better Living" and since its founding has prioritized community impact in each state where its beer is sold. Ninkasi’s “Beer is Love” donations program donates beer to registered 501(c)3 nonprofit organizations, focusing on the core categories of women, equality, recreation, the environment, and arts and music. Ninkasi Studios is located in the brewery complex and was created to foster the talents of young or undiscovered artists. They have also organized music festivals, including the Whiteaker Block Party and Last Band Standing competition.

The Ninkasi Space Program debuted in 2014 when the company launched brewer's yeast into space on a rocket and brewed beer with the yeast when it returned. It took two missions (Mission One in July 2014, Mission Two in October 2014) to yield viable yeast. The space beer, called Ground Control, was released in April 2015 and was an imperial stout made with Oregon hazelnuts, star anise, and cacao nibs fermented with space yeast strains.

Ninkasi has an in-house art department, which designs merchandise, labels, and other promotional materials, as well as its own metal working shop, which creates signs and tap handles.