Uniseed was established as a joint venture pre-seed and seed fund between UQ Holdings Ltd/UniQuest Pty Ltd and Melbourne Ventures Pty Limited (formerly Melbourne University Private), the commercial arms of the University of Queensland and the University of Melbourne, respectively.

It began operations in September 2000 as a $20 million early stage venture fund. In January 2005, Westscheme, Western Australia's largest non-government superannuation fund (a fund for Western Australia public servants is the largest one in this State), invested $15 million into the Uniseed fund. The private investment showed considerable validation of the Uniseed model, and boosted the fund to $35 million.

In December 2005, the University of New South Wales committed $10 million to the fund and the founding Universities contributed a further $8 million each, taking the total committed capital to over $60 million.