Lena Wilson was head-hunted for a position on the board of quality and safety company Intertek, paying a £55,000 salary for working 12 days a year.
This is in addition to her £200,000-a-year post as chief executive of the taxpayer-funded economic development agency.
Crawford Gillies, chairman of Scottish Enterprise, said Ms Wilson's appointment would benefit the body, as it would "build on her commercial awareness and expertise".
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It is the first time a head of Scottish Enterprise has taken on a private sector directorship.
But the leader of the Scottish Liberal Democrats called for an investigation into the "questionable" move, saying it "celebrates" unjustifiably high pay in the public sector and contravenes SNP rhetoric.
William Rennie said: "Many people would have to work three years to earn £55,000 yet Lena Wilson will earn that in 12 days. Does the Chief Executive of the government agency responsible for strengthening business and creating jobs not have enough to do that she has the time to take on extra work? Scottish businesses need all the help they can get."
Mr Rennie said the Scottish Finance Minister's decision to approve the appointment should be investigated, and warned there was a danger of conflicts of interest.
Scottish Enterprise awards about £10,000 a year to projects Intertek is involved with, and Ms Wilson will have to absent herself from those grant-giving decisions.
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