Frayne, who will leave his current role in August, was selected for the education role in February 2011, after heading campaigning for the TaxPayers' Alliance. Before that, he worked at agencies including Portland and Westbourne Communications.
Former colleague and managing partner at Portland, Steve Morris, called Frayne 'unique' in his skillset.
'He is a campaigner to his fingertips, and while he had a good reputation in government, this will take him back to his roots,' he said.
'He was a bold hire, as he didn't fit the conventional civil service profile.'
The DfE has yet to announce a replacement for Frayne.