One of Scotland' s top Covid experts, Prof Bauld will take up the role of interim chief social policy adviser on September 27.
The academic said she looked forward to the part-time secondment, which is expected to last nine months.
"As the immediate threat to health from the virus diminishes at the population level," she explained, “the focus now shifts to Covid recovery.
"I look forward to working with the Scottish government and a wide range of organisations with a particular focus on addressing the social harms arising from the pandemic.”
It is understood Prof Bauld will advise Scottish ministers on reducing poverty and inequality associated with Covid.
She is also an adviser to the Scottish Parliament's Covid-19 committee, and a member of a new expert group assembled by the Scottish Government to plan for future pandemics.
Last Thursday Prof Bauld chaired the first meeting of the standing committee, intended to ensure Scotland is prepared for other new and emerging viruses across the world, which also includes Chief Medical Officer Dr Gregor Smith among its ranks.
Ahead of the meeting she said: “It is critical for scientists and officials to work alongside each other to make sure Scotland can meet the challenges infectious diseases will throw at us in the future.
“I’m delighted to be a part of starting that process.”
Earlier this year Prof Bauld was awarded an OBE for services to Guiding Public Health Response to and Public Understanding of Covid-19 in the Queen's Birthday Honours List.