The Austrian will join the German giants from Austrian Bundesliga side Red Bull Salzburg, where he currently holds the same position, and will take charge from September 1st.
Bayern parted ways with club chief executive officer Oliver Kahn and Hasan Salihamidzic in May, just minutes after they clinched their 11th straight Bundesliga title on the last match of the season.
Freund, who has been at Salzburg for 17 years, will replace Bosnian Salihamidzic at Bayern.
"We are convinced that he is the right person to strengthen the team in the future, together with Thomas Tuchel's coaching team and technical director Marco Neppe," Bayern's CEO Jan-Christian Dreesen said in a statement.
"It has been mutually agreed with Red Bull Salzburg, where Christoph Freund has done an outstanding job, that he will still fully shape the current transfer period with his long-time employer and will not join us until the beginning of September."