Esmarch was born in Tönning, Schleswig-Holstein. He studied at Kiel and Göttingen, and in 1846 became Bernhard Rudolf Konrad von Langenbeck's assistant at the Kiel surgical hospital. He served in the Schleswig-Holstein War of 1848 as junior surgeon, and this directed his attention to the subject of military surgery. He was taken prisoner, but afterwards exchanged, and was then appointed as surgeon to a field hospital. During the truce of 1849 he qualified as "Privatdocent" at Kiel, but on the fresh outbreak of war he returned to the troops and was promoted to the rank of senior surgeon.