In the later half of his life, he worked at several medical institutions in Chicago, and became one of the most highly regarded surgeons in the United States.

However, he did not cope well with the Egyptian climate, and at the advice of a group of Americans he met in Cairo, he set off for the United States.

Fenger's lectures were very popular, and over the years, he trained several prominent physicians, including William James Mayo, Charles Horace Mayo, Nicholas Senn, James B. Herrick, Ludvig Hektoen, and Howard Taylor Ricketts.

[3] In Chicago, Fenger helped demonstrate the bacterial origins of endocarditis and developed techniques for cleft palate repair, vaginal hysterectomy, and the relief of ureteral strictures.

[3] A writer in the Journal of the American Medical Association declared, "There is nothing that he has written, at least nothing with which we are familiar, that does not contain something of value, valuable at least for the time at which it was produced.