The ex-finance secretary will tackle the SNP government’s “top priority” of closing the attainment gap among pupils following a cabinet reshuffle.
The SNP has faced criticism with the country’s education system also falling in international league tables.
Mr Swinney’s predecessor Angela Constance has been moved to the new portfolio of communities, social security and equalities.
The new education secretary will carry out several engagements in the capital before moving on to Stirling University where he will speak to students and lecturers.
Mr Swinney said: “Giving every child in Scotland an excellent education and improving prospects for all our young people is at the heart of the Scottish government’s priorities this term.
“Allocating the deputy first minister the role of education secretary demonstrates the significance that the first minister attaches to this issue.
“Our children and young people must be given the best possible start in life and I am determined to drive forward this agenda every day that I hold this office.
“Today I look forward to engaging directly with children, young people, early years staff, teachers, youth workers, students and lecturers – all of who are key to helping this government in our crucial work to ensure that every child in Scotland can have a great future.”