John Macdonald was born on Christmas Eve 1861, the eldest child of Donald, the owner of an Inverness house-painting business, and Harriett Robertson, born in Auldearn by Nairn. They had married in February that same year. John would attend Inverness Academy, where he played cricket and rugby before, aged seventeen, he headed south to Edinburgh to study medicine. There at summer cricket in 1880 he was part of the Scotland team that played the Australian tourists and in 1884 he captained the university. But with regard to his winter game of choice a switch was made from rugby to football, again captaining the university from centre-half, teams in the East of Scotland having adopted the three-man half-back line, originated in Wales but by then widely adopted in England.     

However, having graduated in 1884 he began to turn out in Glasgow for Queen's Park. There he played eleven times, mainly alongside Charles Campbell on the left of the two-man half-back line employed in the West of Scotland. Those games would include as well as domestic competitions two FA Cup Finals, English FA Cup Finals, in 1884 and 1885, both lost to Blackburn and before Scots teams were from 1885-6 prevented by the SFA from participation. In 1885 he would also represent Glasgow against London and in 1886, once more under the Edinburgh University banner but with Campbell still beside him, he played for Scotland against England, a 1-1 draw at Hampden. It was to be his only cap although there may well have been more had he not decided to return to Inverness to go into medical practice. In 1891 at thirty he was back living with his parents, in 1897 he married a young widow, Isabella "Ella" Mackintosh, with whom he was to have five children. He would also from private practice rise to become Chief Medical Officer for Health for both Inverness Burgh and Inverness County Council.

At home in Inverness, whilst in his leisure time he was still playing cricket, he nevertheless he retained an interest in and influence on football. In 1932 he became a patron of the Highland League. And the McWilliam story is that some thirty-five years earlier Peter had been banned by his father from playing but continued to do so under an assumed name. His father had found out and confiscated the young man's boots until a personal visit from the famed doctor changed the old man's mind. It was a visit that might be said to have changed the shape of World football.