Graduating in 1844, Clarke was commissioned a 2nd Lieutenant in the Royal Engineers and after a year of further study at Chatham was sent to Fermoy in Ireland. In 1846 he was nominated to the Oregon Boundary Commission; his father, who was then governor of Western Australia, urged him instead to come to Australia with the hope of later gaining a professional post with him. As a lieutenant in command of a detachment of Royal Engineers, Clarke sailed with the new lieutenant-governor, Sir William Denison, aboard the "Windermere" and arrived at Hobart on 26 January 1847. His father's death the following next month left Clarke with little reason to remain in Australia but he continued to superintend convict labour and to survey the area around Hobart and design wharf accommodation and became friends with William Denison.