Professor Andrew Scott from Edinburgh University's School of Law began working for the SNP administration on January 3, and his secondment will run for two years.
Some, most notably the Nationalists' opponents, will see his appointment as tacit acknowledgement that Scottish Government ministers have not been well-prepared on the important subject.
Labour said Prof Scott's role showed the SNP was "desperate" to end its blunders. The academic is the partner of SNP MSP Aileen McLeod.
Nicola Sturgeon, the Deputy First Minister, explained Prof Scott would provide advice on ministers' engagement with the European Union and said his counsel would be invaluable to them as they prepared to negotiate the terms of Scotland's entry to the EU, should Scots vote for independence in next year's referendum.
She said: "Andrew Scott is an extremely eminent academic and one of the leading experts on the European Union anywhere in Scotland.
"I am therefore absolutely delighted he has agreed to offer his considerable expertise to ministers in the run-up to the referendum. Professor Scott is a highly respected academic in this field and his help will be invaluable as we prepare to negotiate the terms of Scotland's continuing engagement with the EU from within following a 'yes' vote in the autumn of 2014."
Prof Scott said: "I am very pleased to be joining the Scottish Government on secondment to help deliver a European engagement strategy and to provide expertise on European Union institutions, treaties and policies that will underpin the Scottish Government's approach to defining options for the future."
The academic has acted as expert to various EC agencies, including the European Commission and the Statistical Office of the EU. Prior to joining the University of Edinburgh, he was lecturer in economics at Heriot-Watt University.
He is also a former joint editor of the Journal of Common Market Studies.
Asked how much Prof Scott would be paid, a spokeswoman for the Scottish Government told The Herald: "The agreement will see the Scottish Government reimburse Edinburgh University for the time Prof Scott spends on secondment, i.e. three days a week for the secondment period. The level of Prof Scott's salary is a matter for the university."
She added: "The Scottish Government has always had officials tasked with working on EU issues and has long had a Brussels-based office, pre-dating the current administration."
It is thought Europe is among the "work streams" on which Holyrood officials are working as they prepare various policy papers in the run-up to the White Paper on independence, which the Scottish Government is due to publish in November.