As they set sail, little did they think the youngster would go on to become the country's first Prime Minister.
Now Canada is preparing to mark the 200th anniversary of his birth, in Glasgow's Laurieston, with a series of events.
The young Macdonald moved to Bath Street, then to a flat in Brunswick Lane, next to the Mitre and the Fox and Hound bars, before setting sail for Canada in 1820.
The family's home was demolished many years ago but the site is the focus for Canadians looking to mark the anniversary next year, and a plaque honouring Macdonald can be found in Ramshorn Cemetery in the Merchant City.
The youngster's family emigrated to Kingston, in Upper Canada - today the southern and eastern portions of Ontario - after his father Hugh's unsuccessful business ventures left them in debt. Soon after they arrived, John's younger brother James died from a blow to the head from a servant who was supposed to look after the boys.
After he quit formal school at 15, he needed to start earning immediately to support his family because his father's businesses were again failing, so his parents decided he should be a lawyer.
Macdonald began his apprenticeship with a prominent young lawyer and was called to the Canadian bar in 1836.
He took on dramatic criminal cases, which got him noticed, then entered politics in 1843 when he was appointed to the local council.
The following year he was elected Conservative member of the Legislative Assembly.
Between 1867 and 1873, Macdonald was the first Prime Minister of what is today recognised as Canada and was returned again as Prime Minister from 1878 to 1891.
Plans are under way in Glasgow to mark the anniversary of the birth of the local lad, who went on to become Sir John Macdonald.
A city council spokesman said it is hoped to get a tribute to him at the site of his last home in the city.
The spokesman added: "The city council and, I understand, the Scottish Government are aware that January 11, 2015, marks the 200th anniversary of his birth in Glasgow.
"We will continue to discuss with the site owners what form any commemoration to Sir John may take on the site around Brunswick Lane."