Nick Pearce will replace Tony Benn's son Hilary, who became Leeds Central MP earlier this month.
He will take over responsibility for policy on further and higher education in mid-July.
Mr Pearce is the IPPR's director of education policy. His work at the think-tank included co-writing Wasted Youth, a report on tackling disaffection among young people and overseeing the University for Industry pilot projects.
Before the election, as researcher for Bryan Davies, Labour's further and higher education spokesman, he was heavily involved in developing policy on individual learning accounts and student support. He is highly respected by both Mr Blunkett and Tony Blair.
With Labour desperate to avoid further accusations of cronyism, a number of candidates were interviewed. Lord Irvine, the Lord Chancellor, was recently taken to court over the appointment of his special adviser.
Mr Pearce's knowledge of post-16 education worked in his favour. One of his first tasks will be to build on the Government's post-16 White Paper. Josh Hillman, head of education policy at the BBC and a former colleague of Mr Pearce at the IPPR is believed to have been in the running for the job.
Mr Pearce is the latest of the bright young things who worked for Labour in opposition to make the transition to Government. Mr Blunkett's other special advisers, Conor Ryan, Sophie Linden and Tom Engel all worked for him in opposition.
It will not be Mr Pearce's first taste of Whitehall life. He is currently advising the social exclusion unit on 16 to 18-year-olds' education and, until last summer's reshuffle, he was special adviser to Ann Taylor, then Leader of the House of Commons.