Martyn Harrow, director of information services at Cardiff University, will replace Malcolm Read, who has been in the position since Jisc was formed 18 years ago.
Mr Harrow joined Cardiff in 2003, having previously worked as chief information officer for companies within Unilever.
He said that he would help create a “new Jisc for new times”.
“Our driver will be to ensure that ‘new Jisc’ fosters, facilitates and enables modern approaches and sustainable strategic advantage for higher and further education in the coming years,” Mr Harrow said.
He will take up the post on 1 February 2012 on a nine- to 18-month fixed contract.
In February this year a report by Sir Alan Wilson recommended that Jisc be part funded by institutional subscriptions, rather than mainly by central funding councils as it is now.
The body’s capital funding, which invests in innovation in IT, fell from ?37.5 million in 2007-08 to ?.6 million in 2010-11 and is expected to fall further as funding council budgets shrink.
Dr Read has said that individual institutions might not be willing to contribute to national projects that do not benefit them directly and that there were “grounds for concern that this country won't be as innovative in exploiting IT opportunities” if the new funding model was adopted.
In a statement on the changes of personnel, Jisc says that Dr Read is “looking forward to his planned retirement and more time to pursue his many interests and ambitions”.
Tim O’Shea, principal of the University of Edinburgh and chair of Jisc, said: “Jisc is embarking on an exciting period as it rises to the challenges of the Wilson report and renews its focus on supporting education and research across the UK.
“Martyn is ideally placed to lead Jisc through this stage of its development, being able to draw on invaluable experience from across the education, public and private sectors.”