From 1963 to 1967 Thornett was entrenched as Australia's leader captaining the Wallabies more times than any player to that point in Australia's rugby history. By this point in his career and with his pace slowing, Thornett had moved from flanker to second-row and then settled into the front-row. He captained the Wallabies on the 1962 tour of New Zealand playing in all three Tests and in 11 of the total 13 matches. In 1963 he captained Australia to an 18–9 victory in a one-off Test at the Sydney Cricket Ground against England. Then in 1963 he led the Wallabies on a 24 match tour of South Africa, playing in 16 of the matches including the drawn four Test match series – a highlight of Australia's dour international record over the 50s and 60s. He played in all eight matches of the 1964 tour to New Zealand, including three Tests and then in 1965 he led New South Wales and Australia (twice) to victory over the visiting Springboks, followed the next year by matches at home against the British Lions.