In 1994, Flynn became the Coadjutor Archbishop of Saint Paul and Minneapolis, and succeeded to that see in 1995. He was especially noted for his devotion to Catholic education and the emphasis in his ministry on social justice, especially within his own archdiocese. He was also a strong advocate for Catholic economic justice abroad, and many of the parishes in the archdiocese have sister parishes in impoverished nations, such as Costa Rica. On September 12, 2003, he released a pastoral letter dealing with the issue of racism titled "In God's Image", in which he called for the parishes of the diocese to unite in an effort to end racism and promote diversity and harmony, and in so doing, to make God's love more present to the rest of the world.