In 1854 Esmarch became director of the surgical clinic at Kiel, and in 1857 head of the general hospital and professor at the University of Kiel. During the Schleswig-Holstein War of 1864, Esmarch rendered good service to the field hospitals of Flensburg, Sundewitt and Kiel. In 1866 he was called to Berlin as member of the hospital commission, and also to take the superintendence of the surgical work in the hospitals there. When the Franco-Prussian War broke out in 1870, he was appointed surgeon-general to the army, and afterwards consulting surgeon at the great military hospital near Berlin.