Thomas Cook was baptised at the parish church in Whitchuch, Shropshire, in 1814. In 1826, at the age of 14, he was apprenticed as a clerk to a local solicitor. At the Shrewsbury Assizes in March 1831, Cook and an accomplice, Thomas Salusbury Robinson, were convicted of writing a threatening letter to a Whitchurch auctioneer, William Churton, and Cook was also tried on another charge of writing a similar letter to a conservative peer, Lord Kenyon. This felony was connected to the widespread rural unrest known as the Swing Riots, in which radical groups, protesting against the impoverished condition of agricultural labourers, launched a campaign of intimidation against landowners and industrialists which often included sending threatening letters attributed to the mythical founder of the movement, Captain Swing; these letters coincided with an outbreak of sporadic arson attacks on rural property. The letter that Cook and his co-accused had sent was signed: "Men determined to right the oppressed, Agents to Swing, London." In his autography, Cook downplays the political element of his crime, describing it as a "mere act of youth... done for the sake of sport," but it seems likely that conservative outrage about a number of incidents of arson in the Whitchurch area caused the court to take a far more serious view of the matter. Cook had some reason to be bitter about his treatment relative to his co-accused, Robinson, an older man (who was in fact a relative of the victim) who testified against Cook at the trial. Robinson was recommended for mercy, and given a sentence of two years imprisonment, while Cook, just eighteen years-old, was sentenced to fourteen years' transportation. After some time on the Leviathan hulk, Cook was transported to New South Wales on the Surry, and arrived in Sydney in August 1831.
In Sydney, Cook was employed as a clerk to the storekeeper at the Convict Barracks. According to his own account, he was unfairly punished and removed from this position through the machinations of the new Superintendent of the Barracks, Ernest Augustus Slade, who was quickly to become a controversial Police Magistrate in Sydney. Cook was despatched to hard labour on the road gangs on the outskirts of the Blue Mountains. Entangled in an affair involving the theft and slaughter of some bullocks by his hut-mates, Cook was sentenced to work twelve-months in irons on the road gang based at No. 2 Stockade, Cox's River. He was subsequently sent to Port Macquarie, where he made repeated escape attempts, eventually succeeding in 1836. According to his autobiography, he made it to Paterson's River, where he found work with the settler Andrew Lang, intending to earn enough to pay his passage to Sydney. When recognised by another convict, Cook decided to leave immediately, and attempted to gain a passage by forgery. Arrested for this, Cook managed to escape again before finally being recaptured. Tried for forgery at the Maitland Quarter Sessions in May, 1836, he was sentenced to transportation for life to Norfolk Island.