At Genoa, Fleeming attended the University, and was its first Protestant student. Professor Bancalari was the professor of natural philosophy, and lectured on electro-magnetism, his physical laboratory being the best in Italy. Jenkin took the degree of M.A. with first-class honours, his special subject having been electro-magnetism. The questions in the examinations were put in Latin, and answered in Italian. Fleeming also attended an Art school in the city, and gained a silver medal for a drawing from one of Raphael's cartoons. His holidays were spent in sketching, and his evenings in learning to play the piano; or, when permissible, at the theatre or opera-house; for ever since hearing Rachel recite the Marseillaise at the Theatre Francaise, he had conceived a taste for acting.

In 1850 Fleeming spent some time in a Genoese locomotive shop under Mr. Philip Taylor, of Marseilles; but on the death of his Aunt Anna, who lived with them, Captain Jenkin took his family to England, and settled in Manchester, where the lad, in 1851, was apprenticed to mechanical engineering at the works of Messrs. Fairbairn, and from half-past eight in the morning till six at night had, as he says, 'to file and chip vigorously, in a moleskin suit, and infernally dirty.' At home he pursued his studies, and was for a time engaged with Dr. Bell in working out a geometrical method of arriving at the proportions of Greek architecture. His stay amidst the smoke and bustle of Manchester, though in striking contrast to his life in Genoa, was on the whole agreeable. He liked his work, had the good spirits of youth, and made some pleasant friends, one of them the authoress, Mrs. Gaskell. Even as a boy he was disputatious, and his mother tells of his having overcome a Consul at Genoa in a political discussion when he was only sixteen, 'simply from being well-informed on the subject, and honest. He is as true as steel,' she writes, 'and for no one will he bend right or left... Do not fancy him a Bobadil; he is only a very true, candid boy. I am so glad he remains in all respects but information a great child.'