Anne Glover is currently a biochemist at the University of Aberdeen and has been serving as Scotland's chief scientific adviser since 2006.
Her primary responsibility as EU chief scientific advisor will be to provide high-level, independent, scientific advice to the commission throughout the policy process.
She will report directly to commission president José Manuel Barroso and will be supported by the Bureau of European Policy Advisors (BEPA).
The appointment has been broadly welcomed with Ragnar Löfstedt, professor of risk management and director of the King's Centre for risk management in London, saying, "I am delighted at Anne Glover's new role.
"It presents an opportunity for scientific scrutiny at the European level and will boost the role of science based policy-making.
"This marks a fundamental review of the way in which European institutions access and use science."
He added, "I look forward to seeing a European culture of science, technology and innovation strengthened at the EU level and enhanced public confidence in science and technology."