Logan Douglas was admitted to hospital in Edinburgh, where doctors spotted signs of the rare disease and ordered a test.
Health protection experts said there had not been a report of a baby with botulism in Scotland since electronic record-keeping began in 1983.
Logan has been left paralysed after contracting the disease, which doctors believe he could have contracted through sucking honey from a dummy.
His condition at the Royal Hospital for Sick Children in Edinburgh was described as critical but stable last night, a spokeswoman for NHS Lothian said.
Last night – six weeks after he was first admitted to hospital, in Kirkcaldy, Fife – Logan was on a ventilator.
His mother, Theresa Fitzpatrick, from Dunfermline, said: "We are pleased that he's in the best place to get the treatment he needs, and we hope he will be fit and strong again as soon as possible."
His father, Alex Douglas, said: "He's our bonnie lad, and we are looking forward to getting him back home soon and seeing him smiling again."
Logan was admitted to the hospital on 19 September.
Botulism is caused by a toxin produced by the bacterium Clostridium botulinum. The disease can be fatal in 5 to 10 per cent of cases.
A spokeswoman for Health Protection Scotland said: "Based on our electronic records, which go back to 1983, we have not seen a laboratory report of an infant botulism case.
"There have been no cases of botulism in Scotland in the past year."
According to the Health Protection Agency (HPA), which covers England and Wales, there were two reported cases of infant botulism in 2007 and one case in 2008. There were also six laboratory-reported cases of infant botulism between 1975 and 2006.
Infant botulism was discovered in 1976. There have been just six cases in the UK – one where a baby was fed honey in water – but none in Scotland until now. The last recorded case of infant botulism in the UK was in England in 2001.
A baby girl, aged just four months, contracted the disease on holiday in Spain. It was more than a month before she could be taken off the ventilator.
Expert Professor Nigel Minton, of Nottingham University, said: "Botulism causes massive paralysis. The organism colonises in the gut and produces toxin in infants. It takes a long time to recover.
"It causes damage but the body will eventually repair that damage."
Prof Minton added: "Honey keeps cropping up, particularly in US cases."
INFANTS PRONE TO DISEASE
BOTULISM is a rare but deadly disease which has the power to kill but can be treated with modern drugs.
It is carried by bacteria called Clostridium botulinum. The bacteria do not actually cause symptoms but they create a poison – botulinum toxin – which paralyses nerves and muscles.
It is estimated that just one gram could kill a million people.
Contaminated tinned foods can contain botulinum toxin. As spores, the infection can enter the body through wounds.
Babies are prone to catching botulism because their digestive system is unable to kill off the spores, which can be found in honey. This is why infants are at risk if fed honey before they are a year old.
Despite the danger, the practice of dipping a dummy in honey continues.
The respiratory failure and paralysis that occur with severe botulism may require a patient to be on a ventilator for weeks, with intensive medical and nursing care. After several weeks, the paralysis slowly improves. If diagnosed early, foodborne and wound botulism can be treated with a horse-derived antitoxin, which blocks the action of poison circulating in the blood.
This can prevent patients from deteriorating, but recovery still takes many weeks. Physicians may try to remove contaminated food remaining in the gut by inducing vomiting or by using enemas. Good supportive care in a hospital is the mainstay of therapy for botulism.