Verhaegen is credited with planning the original college building and implementing the plan of studies, as well as being "the mainspring of all its important works and movements.” He also established the first medical school at Saint Louis University, which opened in the fall of 1842.

In 1836 Verhaegen was appointed head of the Missouri Vice-Province, a post he occupied for seven years. He moved the base of Jesuit operations from Florissant to Saint Louis University, chose his dear friend Father Pierre Jean Desmet to minister to the Native Americans, and continued to serve as president of the university´s board of trustees. Verhaegen´s rise continued with a three-year stint as Maryland provincial and a term as the first president of St. Joseph´s College in Bardstown, KY. His life and work came full circle when he returned to Missouri as pastor at St. Charles Borromeo in 1851. He died in St. Charles in 1868.