Two days prior to his death he correctly predicted the findings of his own autopsy: "I think the necropsy will show plaques in my aorta.

A secretary transcribed his words, and they were printed as "The Surgical Clinics of John B. Murphy, M.D., at Mercy Hospital, Chicago".

[10] Early in his career, on May 4, 1886, he was one of the doctors summoned to the scene of the Haymarket Affair in the Near West Side community area of Chicago.

[11] A bomb had been thrown at the Chicago Police officers leading to several deaths and a high-profile trial, in which Murphy was called to testify.

"[5] Although his surgical prowess was not questioned, his approach to practice was considered pretentious by a segment of his professional colleagues in the U.S.,[4] and his work was more highly regarded by his contemporaries in Europe than in Chicago.

[4][8] Murphy developed his eponymous anastomotic button for a sutureless anastomosis of the gallbladder to the duodenum (his preferred treatment for acute cholecystitis), but it was equally suitable for intestinal anastomoses.

The Murphy button can be credited as the forerunner of the modern end-to-end stapling instrument after having become the method of choice for operations at the Mayo Clinic and elsewhere in the United States for over twenty years.

[8] In 1898, Murphy was first in the United States to induce artificial immobilization and collapse of the lung (pneumothorax) in treatment of pulmonary tuberculosis.

[4][8] He was also considered an innovator for surgical intervention for prostate cancer, performance of end-to-end anastomosis of hollow viscera.

[1] He was knighted with the Order of St. Gregory the Great at the direction of Pope Benedict XV by Archbishop George Mundelein on June 16, 1916.

[1] The John B. Murphy Public School in the Irving Park community on the northwest side of Chicago, which opened in 1924, was named in his honor.