After service in the United States Army Air Corps during World War II, Murphy returned to The Post but soon acquired the Citizen Newspapers, a group of neighborhood papers in Houston Heights. Oilman Glenn H. McCarthy, the "King of the Oil Wildcatters" who also built the Shamrock Hotel in Houston bought the Citizen group in 1948. Murphy then became the editor of fourteen small newspapers.
In 1952, Murphy became executive director of the Texas Daily Newspaper Association, where he remained until his first retirement in 1984. Shortly thereafter, he joined Richard Johnson at The Chronicle as administrative assistant. He drafted speeches for Johnson and scrutinized other newspapers for ideas. He retired again in 2005.
Murphy was an active member of the First United Methodist Church in Houston and served on the committee that established the church's Westchase campus.
He authored several books, two of which were biographies: The Man Who Dug the Well, about publisher Dick Johnson, and The Legend and Legacy of Dr. William H. Hinson (1902-1977), former pastor of First United Methodist Church of Houston. Murphy was married three times. His first wife, the former Ernestine "Ernie" Lampson (1913-1977), was an All-American basketball guard for the "Cardinals" in Durant, Oklahoma, who moved to Galveston to play for an insurance company team. The couple married in the home of Murphy's parents on April 29, 1939. The couple had two children: John Hulen Murphy, II (born 1944), of Austin, and Lynn Murphy Graeter (born 1948) of Houston. His second marriage, to Virginia Hobson of Houston, ended in divorce. His third wife, the former Nancy Neal, died in 2003.
Murphy died at his Houston home after a brief illness. In addition to his children, he had three stepsons from his third wife, Todd Neal and Scott Neal, both of Houston, and John Neal, of Hattiesburg, Mississippi. Services were held at the First United Methodist Church Westchase Campus. Burial was in Forest Park Lawndale Cemetery in Houston. Nelson Clyde, IV, the publisher of the Tyler Morning Telegraph in Tyler, issued this statement on Murphy's death: "John was one of the first people I met in my earliest experience with Texas Daily Newspaper Association. He has been a friend to my father (Nelson Clyde, III) and grandfather for many years, and we have enjoyed his guidance at TDNA meetings. His vast contacts will surely remember him as a kind and decent person. . . . " According to Charles Moser of the Brenham Banner Press in Brenham, the seat of Washington County south of Bryan-College Station, "The passing of John Murphy at the age of ninety-four is really the end of an era for the Texas newspaper industry. "He had a huge role in promoting the newspaper industry during a time of great growth when he served TDNA from 1952 to 1984."
The TDNA established the John Murphy Award to honor outstanding copy editors.