[2] Murphy was to remain at the college for thirteen years in the role of rector or president (the use of one title over the other was fairly contentious at the time).

[5] Murphy enlarged the Classics and Commercial departments, and added courses in dramatics, debating, and elocution; the college's first bachelor's degrees were conferred in 1889.

[5] Murphy's great love of public speaking inspired him to personally direct a production of Euripides' Alcestis in the original Greek in 1891.

Though that sort of production was not well-suited to Pittsburgh's working-class population, the play was a success, and earned the college $1,000—most likely because Murphy had decided to provide verbal introductions in English before each act.

[6] Another shrewd decision was made when the South Fork Hunting and Fishing Club's dam broke on the Conemaugh River in 1889, causing the Johnstown Flood.

[7] Murphy serving as the superior of the Holy Ghost Fathers's community in Pittsburgh from 1893 to 1899, during which time he was much in demand as a lecturer on education.

[2] He made the acquaintance of many influential Catholic leaders in America: he was asked by Cardinal James Gibbons to open a school in Baltimore, and by Bishop Michael O'Connor to found one in Philadelphia.

[2] He assisted at the foundation of Catholic University in Washington, D.C.[2] Further associations included Archbishop John Ireland of Saint Paul, Minnesota, and Mother Katharine Drexel,[2] who was later to be canonised in 2000.

Murphy made an attempt to convert Margaret Anna Cusack, called "the Nun of Kenmare", back to Catholicism in the last years of her life, but failed, to substantial public embarrassment.

[2] Nonetheless, he spent two years there, and was called on to lecture to the Catholic students at the University of Oxford, where his talk on theological modernism was well received.

In an effort to expand his activities there, he made a deal with the wealthy Mother Drexel—in return for money, he would send twenty Spiritan scholastics to help her in her ministry to America's African American population.