Around 1906 Murphy assisted Frank Chapman at the American Museum of Natural History and read the proofs of Warblers of North America.
[2] In 1951, Murphy led the expedition that rediscovered the Bermuda petrel, or cahow, a bird believed to have been extinct for 330 years.
He was elected a Corresponding Member of the Royal Australasian Ornithologists' Union in 1939 and the American Philosophical Society in 1946.
[4] After Murphy's retirement to Old Field, New York, in 1957, he, along with other citizens of Long Island including Archibald Roosevelt, unsuccessfully sued to stop the spraying of DDT.
Murphy accompanied Arthur Vernay to the island of Inagua in 1956 to look at the flamingo colony there during which they were joined by Ian Fleming upon whom he would make an impression.
Murphy was an avid diarist, even maintaining duplicates of every check he wrote so as to help any future research.
Trachurus murphyi, the Chilean jack mackerel, is named in honor of Murphy who collected the type off Peru.