The two clubs will "exchange talent", allowing players to experience both the coaching in place at Bayern and at the MLS club.
“The United States is home to our very first international office, highlighting our commitment to engaging and growing FC Bayern’s fan base in the Americas,” said Bayern’s Executive Board Member for Internationalization and Strategy, Jörg Wacker.
“Our intention from the beginning has been to help support the growth of soccer in the U.S., supporting the existing development of players. For us FC Dallas is the ideal partner."
The two clubs will also create fixtures that will allow the young players to play against each other, in both Germany and America.
"We are thrilled to join FC Bayern Munich in this groundbreaking collaboration," said FC Dallas chairman and CEO Clark Hunt.
"One of our primary goals is to develop an academy and a club that can compete at the highest level on a global scale. This unprecedented partnership with one of the most successful clubs in the world marks a significant step toward that goal, and we look forward to working closely with the outstanding leadership at FC Bayern."
Twenty academy players signed for Dallas' first-team - an MLS high - and at least 28 players from the club's youth set-up have been capped by the United States, Canada or Mexico at youth level.
Three homegrown players of the club have already been sent to Germany, including 17-year-old Paxton Pomykal, who became the club's youngest ever starter in March.