He attended Newington College (1974–1979)  and St Andrew's College within the University of Sydney. Not selected for the First XV at Newington, Farr-Jones played his early first grade rugby for Sydney University and worked as a lawyer when rugby was an amateur sport.
Selected for the 1984 tour of Europe, he made his international début for the Wallabies on 3 November 1984 v England at Twickenham, which Australia won 19-3 and quickly established himself as a regular in the test side from then on, scoring a his first try in the final test against Scotland. After playing in the 1986 Bledisloe Cup series win against the All Blacks, he played in the inaugural Rugby World Cup in 1987 and a year later was named Australian captain, at the age of 25. By this stage he was known as one part of Australia's "holy trinity" (the other two being David Campese and Michael Lynagh). Indeed, of Campese's then world record 64 international tries, Farr-Jones had a hand in 46 of them. His captaincy started well enough with a two test home series win against England but Australia were well beaten in the 1988 Bledisloe and in 1989 lost the series to the British Lions. His temperament under pressure was questioned, though he was the subject of particularly nasty and provocative foul by opposite number Robert Jones, who in an effort to unsettle him, stamped a studded boot onto the top of Farr-Jones' right foot, which had recently been injured. More pressure followed in 1990 after the Wallabies were down 2-0 in the Bledisloe series it seemed certain he would lose the captaincy but the side won the final test 21-9 in Wellington and he celebrated with a naked swim in Wellington Harbour. The 1991 Bledisloe series was closely fought, ending in a tie and the Wallabies arrived in the British Isles in good form for the World Cup. He carried a knee injury into the tournament and was rested for the pool game against Samoa and substituted in the quarter-final midway through the second-half with what looked like a serious injury. After that nail biting finish he was back for the semi-final against New Zealand and the final, won by Australia, of which he said "We had to tackle till our shoulders were red raw just to keep them out". He was also instrumental in 1992 for the Wallabies, with wins over the All Blacks in the Bledisloe Cup and the Springboks in Cape Town, a win that ended doubts over the Wallabies claim to be the best team in the world. He briefly retired from the sport at this stage but was persuaded back for the final two homes tests against South Africa in 1993, after Australia lost the opening match in the series. Farr-Jones was capped 63 times for Australia, including 36 as captain (then a world record), and scored nine tries. During his career, he formed a world record half-back combination with Michael Lynagh of 47 Tests together.
2011: Inducted into the IRB Hall of Fame alongside all other Rugby World Cup-winning captains and head coaches from the tournament's inception in 1987 through 2007 (minus the previously inducted John Eales)