Kocher was born on August 25, 1841 in Bern, Switzerland. His father was Jakob Alexander Kocher, a railway engineer, who moved in 1845 to Burgdorf, Switzerland because of his job as regional engineer of Emmental (Bezirksingenieur). He was named chief engineer for street and water in the canton of Bern at an age of only 34 years and he moved with his family to the capital, the city of Bern. In 1858 he left the states service and managed several engineering projects around Bern. Theodor Kocher's mother was Maria Kocher (née Wermuth), living from 1820 to 1900. She was a very religious woman and part of the Moravian Church; together with Jakob Alexander, she raised a family of five sons and one daughter (Theodor Kocher was the second son).