Bowen was William McMahon's preferred candidate to replace William Owen on the High Court, but Anthony Mason was eventually chosen as it was feared that the Liberal Party would not be able to retain Bowen's seat at a by-election. When McMahon resigned after the 1972 election, Bowen lost the resulting leadership vote by one vote to Billy Snedden, on the fifth ballot. In 1973, Bowen was appointed as Chief Judge in Equity in the Supreme Court of New South Wales. He was appointed first Chief Judge (later Chief Justice) of the Federal Court of Australia in 1976 and held this until his retirement in 1990. Bowen was one of only six politicians to have served in both the Parliament of Australia and the Federal Court of Australia, alongside Bob Ellicott, Merv Everett, Tony Whitlam, John Reeves and Duncan Kerr. Bowen was appointed a Knight Commander of the Order of the British Empire in 1976 and a Companion of the Order of Australia in 1988. He died in 1994, aged 83.