His siblings included Louisa Pierpont Morgan (1866–1946), who married Herbert L. Satterlee (1863–1947), Juliet Pierpont Morgan (1870–1952) who married william Pierson Hamilton (1869–1950), and Anne Tracy Morgan (1873–1952), a philanthropist. His paternal grandparents were Junius Spencer Morgan (1813–1890) and Juliet Pierpont (1816–1884), the daughter of John Pierpont.

Morgan was born on September 7, 1867 in Irvington, New York to J. P. Morgan and Frances Louisa Tracy. He graduated from St. Paul's School and later, Harvard College, in 1886, where he was a member of the Delphic Club, formerly known as the Delta Phi.

In 1890, Morgan married Jane Norton Grew (d. 1925), daughter of Boston banker and mill owner Henry Sturgis Grew. She was the aunt of Henry Grew Crosby. The couple raised four children:

The younger Morgan resembled his Father in his dislike for publicity and continued his father's philanthropic policy. In 1905, his Father acquired the Guaranty Trust bank as part of his efforts to consolidate banking in New York City. After his Father died in 1913, the bank became Jack's base.

At the beginning of World War I, US Treasury Secretary william McAdoo and others in the Wilson administration were very suspicious of J. P. Morgan & Co.'s enthusiastic role as British agent for purchasing and banking. When the United States entered the war, this gave way to close collaboration, in the course of which Morgan received financial concessions. From 1914 to 1919, he was a member of the advisory council for the Federal Reserve Bank of New York.

On 3 July 1915, an intruder, Eric Muenter, entered Morgan's Long Island mansion and shot him twice. This was ostensibly to bring about an embargo on arms, and in protest of his profiteering from war. Morgan, however, quickly recovered from his wounds.

After World War I and the Versailles Treaty, Morgan Guaranty managed Germany's reparation payments. After the war, Morgan made several trips to Europe to investigate and report on financial conditions there. In 1919 he was for a time chairman of the international committee, composed of American, British and French Bankers, for the protection of the holders of Mexican securities. In November 1919, he was made a Director of the Foreign Finance Corporation, which was organized to engage in the investment of funds chiefly in foreign enterprises. By the 1920s, Morgan Guaranty had become one of the world's most important banking institutions, as a leading lender to Germany and Europe. He attempted to defeat Franklin D. Roosevelt's plan for the New Deal during the Great Depression, and secured about US$100 million in loans to Italian Fascist dictator Benito Mussolini prior to World War II. Morgan triggered discussion about banking and tax law in at least two areas. First, the fact that he paid no taxes in 1931 and 1932 raised questions about tax law. Second, his activities as a banker raised questions about the responsibility to act for, rather than against, the best interest of depositors.

In 1920, Morgan gave his London residence, 14 Princes Gate (near Imperial College London), to the U.S. government for use as its embassy.

In 1924, Morgan created the Pierpont Morgan Library as a public institution as a memorial to his Father. Belle da Costa Greene, Morgan's personal librarian, became the first Director and continued the aggressive acquisition and expansion of the collections of illuminated manuscripts, authors' original manuscripts, incunabula, prints, and drawings, early printed Bibles, and many examples of fine bookbinding. Today the library is a complex of buildings which serve as a museum and scholarly research center.

A yachtsman, like his Father, Morgan served as commodore of the New York Yacht Club from 1919 to 1921. In 1930, he built the turbo electric driven yacht Corsair IV at Bath Iron Works in Maine. Corsair IV, launched April 10, 1930, was one of the most opulent yachts of its day and the largest built in the United States with an overall length of 343 feet (104.5 m), 42 feet (12.8 m) beam and 2,142 GRT. Legend at the shipyard credits the phrase "If you have to ask, you can't afford it" to Morgan, when asked what the yacht cost. However, this quote is most often attributed to his Father in connection with the yacht Corsair, launched in 1891. Morgan sold the Corsair IV to the British Admiralty in 1940 for one dollar to assist with Britain's war effort. After the war the Corsair IV was sold to Pacific Cruise Lines and, on September 29, 1947, began Service as a luxury cruise ship operating between Long Beach, California and Acapulco, Mexico. On November 12, 1949 the yacht struck a rock near the beach in Acapulco and, although all passengers and crew were rescued, was deemed a total loss.