Soon after his homecoming, Cockerell set up an architectural business of his own in Old Burlington Street, having come to terms with the need to earn his living by the only profession for which he was equipped, and in 1819, he was appointed Surveyor to St Paul's Cathedral. He wrote a detailed account of his expenditure during the last four years of his absence, the years which he had added to the original plan for three years of travel, and this he sent to his father, but Samuel responded by describing how he was treating all of his children. Cockerell seems to have offered to re-pay his father nearly a thousand pounds, the sum which he had spent during the years he had stayed abroad beyond the originally agreed three, but his father refused, and probably continued to give him support. While it would be an exaggeration to say his health had been ruined while he was away, he was to suffer from difficult stomach upsets, which may have stemmed partly from the illnesses he went through, and the medicines he took for them.

Cockerell spent some time working up his drawings of antiquities for exhibition at the Royal Academy, and sorting out his site records. The promised casts of the Aegina marbles were working their way through the Bavarian bureaucracy, delayed by questions of whether they should take the figures before or after Thorvaldsen's restoration, and by Wagner's general desire to cut corners. His reputation had preceded him, and his homecoming was greeted publically, both the Edinburgh Magazine and the Quarterly Journal of Sciences and the Arts reporting his successes in Greece. At the forefront of his mind were plans to publish all that he had accomplished abroad, and he was aware that this needed to be done as soon as possible.

All the time Cockerell was away, he, and Haller also, had been anxious that other people and their publications should not steal their thunder. In 1815, he learnt from the Germans that the Prince of Bavaria had allowed Wagner to publish some sketches of the Bassae sculptures, which he had been given on the understanding that they were strictly for his own use only. Their names were not mentioned, as if, they felt, they were merely the accidental finders of things they did not understand.