He and his mother moved to her parents' home in Dumbarton, and she soon became a public health inspector in Glasgow.
Cronin was not only a precocious student at Dumbarton Academy who won many prizes in writing competitions, but also an excellent athlete and footballer. From an early age he was an avid golfer, and he enjoyed the sport throughout his life. He also loved salmon fishing.
The family later moved to Yorkhill, Glasgow, where Cronin attended St Aloysius' College in the Garnethill area of the city. He played football for the First XI there, an experience he included in one of his last novels, The Minstrel Boy. A family decision that he should study either to join the church or to practise medicine was settled by Cronin himself when he chose "the lesser of two evils". He won a Carnegie scholarship to study medicine at the University of Glasgow in 1914. He was absent in 1916–1917 for naval service. In 1919 he graduated, with highest honours, with the degree of MBChB. Later that year he made a trip to India as ship's surgeon on a liner. Cronin went on to earn additional qualifications, including a Diploma in Public Health (1923) and his MRCP (1924). In 1925 he was awarded an MD by the University of Glasgow for his dissertation, entitled "The History of Aneurysm".